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Volumn 3, Issue 12, 2013, Pages 2105-2114

Increased genomic prediction accuracy in wheat breeding through spatial adjustment of field trial data

Author keywords

GBLUP; Genomic selection; Genotyping by sequencing; GenPred; Quantitative trait locus; Shared data resources; Single nucleotide polymorphism; Spatial correction; Wheat

Indexed keywords

MOLECULAR MARKER;

EID: 84890809438     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.007807     Document Type: Article
Times cited : (74)

References (62)
  • 1
    • 0038444113 scopus 로고    scopus 로고
    • The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms
    • Akhunov, E. D., A. W. Goodyear, S. Geng, L. L. Qi, B. Echalier et al., 2003 The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genet. Res. 13: 753-763.
    • (2003) Genet. Res. , vol.13 , pp. 753-763
    • Akhunov, E.D.1    Goodyear, A.W.2    Geng, S.3    Qi, L.L.4    Echalier, B.5
  • 3
  • 5
    • 58849088886 scopus 로고    scopus 로고
    • QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review
    • Buerstymayr, H., T. Ban, and J. A. Anderson, 2009 QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review. Plant Breed. 128: 1-26.
    • (2009) Plant Breed. , vol.128 , pp. 1-26
    • Buerstymayr, H.1    Ban, T.2    Anderson, J.A.3
  • 6
    • 84856866301 scopus 로고    scopus 로고
    • Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers
    • Burgueño, J., G. de los Campos, K. Weigel, and J. Crossa, 2012 Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers. Crop Sci. 52: 707-719.
    • (2012) Crop Sci. , vol.52 , pp. 707-719
    • Burgueño, J.1    de los Campos, G.2    Weigel, K.3    Crossa, J.4
  • 8
    • 78650614679 scopus 로고    scopus 로고
    • Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)
    • Chao, S., J. Dubcovsky, J. Dvorak, M. C. Luo, S. P. Baenziger et al., 2010 Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 11: 727-744.
    • (2010) BMC Genomics , vol.11 , pp. 727-744
    • Chao, S.1    Dubcovsky, J.2    Dvorak, J.3    Luo, M.C.4    Baenziger, S.P.5
  • 9
    • 42149135435 scopus 로고    scopus 로고
    • Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials
    • Chapman, S. C., 2008 Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials. Euphytica 161: 195-208.
    • (2008) Euphytica , vol.161 , pp. 195-208
    • Chapman, S.C.1
  • 10
    • 18744372502 scopus 로고    scopus 로고
    • An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts
    • Collard, B. C. Y., M. Z. Z. Jahufer, J. B. Brouwer, and E. C. K. Pang, 2005 An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142: 169-196.
    • (2005) Euphytica , vol.142 , pp. 169-196
    • Collard, B.C.Y.1    Jahufer, M.Z.Z.2    Brouwer, J.B.3    Pang, E.C.K.4
  • 11
    • 40949130394 scopus 로고    scopus 로고
    • Marker-assisted selection: an approach for precision plant breeding in the twenty-first century
    • Collard, B. C., and D. J. Mackill, 2008 Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil. Trans. R. Soc. Lond. B Biol. Sci. 363: 557-572.
    • (2008) Phil. Trans. R. Soc. Lond. B Biol. Sci. , vol.363 , pp. 557-572
    • Collard, B.C.1    Mackill, D.J.2
  • 12
    • 33746061693 scopus 로고    scopus 로고
    • Modeling genotype × environment interaction using additive genetic covariances of relatives for predicting breeding values of wheat genotypes
    • Crossa, J., J. Burgueño, P. L. Cornelius, G. McLaren, R. Trethowan et al., 2006 Modeling genotype × environment interaction using additive genetic covariances of relatives for predicting breeding values of wheat genotypes. Crop Sci. 46: 1722-1733.
    • (2006) Crop Sci. , vol.46 , pp. 1722-1733
    • Crossa, J.1    Burgueño, J.2    Cornelius, P.L.3    McLaren, G.4    Trethowan, R.5
  • 13
    • 78649325488 scopus 로고    scopus 로고
    • Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers
    • Crossa, J., G. de los Campos, P. Perez, D. Gianola, J. Burgueño et al., 2010 Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186: 713-724.
    • (2010) Genetics , vol.186 , pp. 713-724
    • Crossa, J.1    de los Campos, G.2    Perez, P.3    Gianola, D.4    Burgueño, J.5
  • 14
    • 0031919890 scopus 로고    scopus 로고
    • Spatial analysis of multi-environment early generation variety trials
    • Cullis, B., B. Gogel, A. Verbyla, R. Thompson, and A. Verbyla, 1998 Spatial analysis of multi-environment early generation variety trials. Biometrics 54: 1-18.
    • (1998) Biometrics , vol.54 , pp. 1-18
    • Cullis, B.1    Gogel, B.2    Verbyla, A.3    Thompson, R.4    Verbyla, A.5
  • 15
    • 78951477718 scopus 로고    scopus 로고
    • Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods
    • de los Campos, G., D. Gianola, G. J. Rosa, K. A. Weigel, and J. Crossa, 2010 Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods. Genet. Res. 92: 295-308.
    • (2010) Genet. Res. , vol.92 , pp. 295-308
    • de los Campos, G.1    Gianola, D.2    Rosa, G.J.3    Weigel, K.A.4    Crossa, J.5
  • 16
    • 33745887838 scopus 로고    scopus 로고
    • Zonas agroclimáticas y sistemas productivos de la VII y VII región
    • Instituto de Investigaciones Agropecuarias. Serie Quilamapu 113
    • del Pozo, A., and P. del Canto, 1999 Zonas agroclimáticas y sistemas productivos de la VII y VII región. Instituto de Investigaciones Agropecuarias. Serie Quilamapu 113.
    • (1999)
    • del Pozo, A.1    del Canto, P.2
  • 17
    • 0030047516 scopus 로고    scopus 로고
    • Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L
    • Dubcovsky, J., M. C. Luo, G. Y. Zhong, R. Bransteitter, A. Desai et al., 1996 Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143: 983-999.
    • (1996) Genetics , vol.143 , pp. 983-999
    • Dubcovsky, J.1    Luo, M.C.2    Zhong, G.Y.3    Bransteitter, R.4    Desai, A.5
  • 18
    • 0025632914 scopus 로고
    • Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes
    • Dvorak, J., and H. B. Zhang, 1990 Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc. Natl. Acad. Sci. USA 87: 9640-9644.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 9640-9644
    • Dvorak, J.1    Zhang, H.B.2
  • 19
    • 0027272045 scopus 로고
    • The evolution of polyploid wheats: identification of the A genome donor species
    • Dvorak, J., P. Terlizzi, H. B. Zhang, and P. Resta, 1993 The evolution of polyploid wheats: identification of the A genome donor species. Genome 36: 21-31.
    • (1993) Genome , vol.36 , pp. 21-31
    • Dvorak, J.1    Terlizzi, P.2    Zhang, H.B.3    Resta, P.4
  • 20
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto 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
    • 85136354327 scopus 로고    scopus 로고
    • Ridge regression and other kernels for genomic selection with R package rrBLUP
    • Endelman, J. B., 2011 Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome J. 4: 250-255.
    • (2011) Plant Genome J. , vol.4 , pp. 250-255
    • Endelman, J.B.1
  • 22
    • 84890813957 scopus 로고    scopus 로고
    • FAOSTAT, Home page. Accessed October 8, 2013
    • FAOSTAT, 2011. Home page. Available at: http://faostat.fao.org/site/339/default.aspx. Accessed October 8, 2013.
    • (2011)
  • 23
    • 8444231488 scopus 로고    scopus 로고
    • Exploratory model selection for spatially designed experiments - some examples
    • Federer, W. T., 2003 Exploratory model selection for spatially designed experiments - some examples. J. Data Sci. 1: 231-248.
    • (2003) J. Data Sci. , vol.1 , pp. 231-248
    • Federer, W.T.1
  • 24
    • 84866362330 scopus 로고    scopus 로고
    • I.4 screening experimental designs for quantitative trait loci, association mapping, genotype-by environment interaction, and other investigations
    • Federer, W. T., and J. Crossa, 2012 I.4 screening experimental designs for quantitative trait loci, association mapping, genotype-by environment interaction, and other investigations. Front. Physiol. 3: 1-8.
    • (2012) Front. Physiol. , vol.3 , pp. 1-8
    • Federer, W.T.1    Crossa, J.2
  • 25
    • 0037274690 scopus 로고    scopus 로고
    • On marker-assisted prediction of genetic value: beyond the ridge
    • Gianola, D., M. Perez-Enciso, and M. A. Toro, 2003 On marker-assisted prediction of genetic value: beyond the ridge. Genetics 163: 347-365.
    • (2003) Genetics , vol.163 , pp. 347-365
    • Gianola, D.1    Perez-Enciso, M.2    Toro, M.A.3
  • 26
    • 45849117254 scopus 로고    scopus 로고
    • Reproducing kernel Hilbert spaces regression methods for genomic assisted prediction of quantitative traits
    • Gianola, D., and J. B. van Kaam, 2008 Reproducing kernel Hilbert spaces regression methods for genomic assisted prediction of quantitative traits. Genetics 178: 2289-2303.
    • (2008) Genetics , vol.178 , pp. 2289-2303
    • Gianola, D.1    van Kaam, J.B.2
  • 27
    • 80053594474 scopus 로고    scopus 로고
    • Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat
    • Gianola, D., H. Okut, K. A. Weigel, and G. J. Rosa, 2011 Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat. BMC Genet. 12: 87-101.
    • (2011) BMC Genet. , vol.12 , pp. 87-101
    • Gianola, D.1    Okut, H.2    Weigel, K.A.3    Rosa, G.J.4
  • 28
    • 80755167697 scopus 로고    scopus 로고
    • Using the genomic relationship matrix to predict the accuracy of genomic selection
    • Goddard, M. E., B. J. Hayes, and T. H. E. Meuwissen, 2011 Using the genomic relationship matrix to predict the accuracy of genomic selection. J. Anim. Breed. Genet. 128: 409-421.
    • (2011) J. Anim. Breed. Genet. , vol.128 , pp. 409-421
    • Goddard, M.E.1    Hayes, B.J.2    Meuwissen, T.H.E.3
  • 30
    • 85167520539 scopus 로고    scopus 로고
    • Genomic selection accuracy using multifamily prediction models in a wheat breeding program
    • Heffner, E. L., J.-l. Jannink, and M. E. Sorrells, 2011 Genomic selection accuracy using multifamily prediction models in a wheat breeding program. Plant Genome J. 4: 65-75.
    • (2011) Plant Genome J. , vol.4 , pp. 65-75
    • Heffner, E.L.1    Jannink, J.-L.2    Sorrells, M.E.3
  • 31
    • 0037734547 scopus 로고    scopus 로고
    • Heritability for plant breeding: an update
    • edited by J. Janick. John Wiley & Sons, Inc., Oxford, UK
    • Holland, J. B., W. E. Nyquist, and C. T. Cervantes-Martínez, 2003 Heritability for plant breeding: an update, pp. 92112, in Plant Breeding Reviews, Vol. 22, edited by J. Janick. John Wiley & Sons, Inc., Oxford, UK.
    • (2003) Plant Breeding Reviews , vol.22 , pp. 92112
    • Holland, J.B.1    Nyquist, W.E.2    Cervantes-Martínez, C.T.3
  • 32
    • 0027247860 scopus 로고
    • Interval mapping of multiple quantitative trait loci
    • Jansen, R., 1993 Interval mapping of multiple quantitative trait loci. Genetics 135: 205-211.
    • (1993) Genetics , vol.135 , pp. 205-211
    • Jansen, R.1
  • 33
    • 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
  • 35
    • 5144221069 scopus 로고    scopus 로고
    • Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars
    • Kraakman, A. T. W., R. E. Niks, P. M. M. M. Van den Berg, P. Stam, and F. A. Van Eeuwijk, 2004 Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446.
    • (2004) Genetics , vol.168 , pp. 435-446
    • Kraakman, A.T.W.1    Niks, R.E.2    Van den Berg, P.M.M.M.3    Stam, P.4    Van Eeuwijk, F.A.5
  • 36
    • 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
  • 37
    • 34547488367 scopus 로고    scopus 로고
    • Molecular markers: actual and potential contributions to wheat genome characterization and breeding
    • Landjeva, S., V. Korzun, and A. Börner, 2007 Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica 156: 271-296.
    • (2007) Euphytica , vol.156 , pp. 271-296
    • Landjeva, S.1    Korzun, V.2    Börner, A.3
  • 38
    • 84860872860 scopus 로고    scopus 로고
    • Genomewide association analysis to identify chromosomal regions determining components of earliness in wheat
    • Le Gouis, J., J. Bordes, C. Ravel, E. Heumez, S. Faure et al., 2012 Genomewide association analysis to identify chromosomal regions determining components of earliness in wheat. Theor. Appl. Genet. 124: 597-611.
    • (2012) Theor. Appl. Genet. , vol.124 , pp. 597-611
    • Le Gouis, J.1    Bordes, J.2    Ravel, C.3    Heumez, E.4    Faure, S.5
  • 39
    • 84866157770 scopus 로고    scopus 로고
    • Getting the most out of sorghum low-input field trials in West Africa using spatial adjustment
    • Leiser, W. L., H. F. Rattunde, H.-P. Piepho, and H. K. Parzies, 2012 Getting the most out of sorghum low-input field trials in West Africa using spatial adjustment. J. Agron. Crop Sci. 198: 349-359.
    • (2012) J. Agron. Crop Sci. , vol.198 , pp. 349-359
    • Leiser, W.L.1    Rattunde, H.F.2    Piepho, H.-P.3    Parzies, H.K.4
  • 41
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Meuwissen, T. H., B. J. Hayes, and M. E. Goddard, 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.1    Hayes, B.J.2    Goddard, M.E.3
  • 42
    • 78649591333 scopus 로고    scopus 로고
    • Arrangement of check plots in augmented block designs when spatial analysis is used
    • Müller, B. U., A. Schützenmeister, and H.-P. Piepho, 2010 Arrangement of check plots in augmented block designs when spatial analysis is used. Plant Breed. 129: 535-542.
    • (2010) Plant Breed. , vol.129 , pp. 535-542
    • Müller, B.U.1    Schützenmeister, A.2    Piepho, H.-P.3
  • 43
    • 78650725232 scopus 로고    scopus 로고
    • Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.)
    • Neumann, K., B. Kobiljski, S. Denčić, R. K. Varshney, and A. Börner, 2010 Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol. Breed. 27: 37-58.
    • (2010) Mol. Breed. , vol.27 , pp. 37-58
    • Neumann, K.1    Kobiljski, B.2    Denčić, S.3    Varshney, R.K.4    Börner, A.5
  • 44
    • 1042304216 scopus 로고    scopus 로고
    • APE: analyses of phylogenetics and evolution in R language
    • Paradis, E., J. Claude, and K. Strimmer, 2004 APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 45
    • 53549118281 scopus 로고    scopus 로고
    • Accounting for spatial variability in field experiments on tea
    • Peiris, T. U. S., S. Samita, and W. H. D. Veronica, 2008 Accounting for spatial variability in field experiments on tea. Exp. Agric. 44: 547-557.
    • (2008) Exp. Agric. , vol.44 , pp. 547-557
    • Peiris, T.U.S.1    Samita, S.2    Veronica, W.H.D.3
  • 46
    • 77956970196 scopus 로고    scopus 로고
    • Linear variance models for plant breeding trials
    • Piepho, H. P., and E. R. Williams, 2010 Linear variance models for plant breeding trials. Plant Breed. 129: 1-8.
    • (2010) Plant Breed. , vol.129 , pp. 1-8
    • Piepho, H.P.1    Williams, E.R.2
  • 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, J. A., P. J. Brown, M. E. Sorrells, and J. L. Jannink, 2012a 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
  • 49
    • 84875444971 scopus 로고    scopus 로고
    • Genotyping-by-sequencing for plant breeding and genetics
    • Poland, J. A., and T. W. Rife, 2012 Genotyping-by-sequencing for plant breeding and genetics. Plant Genome J. 5: 547-557.
    • (2012) Plant Genome J. , vol.5 , pp. 547-557
    • Poland, J.A.1    Rife, T.W.2
  • 51
    • 84907095419 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • R Development Core Team, Vienna
    • R Development Core Team, 2008 R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available at: http://www.R-project.org.
    • (2008) R Foundation for Statistical Computing
  • 53
    • 0029741063 scopus 로고    scopus 로고
    • The future of genetic studies of complex human diseases
    • Risch, N., and K. Merikangas, 1996 The future of genetic studies of complex human diseases. Science 273: 1516-1517.
    • (1996) Science , vol.273 , pp. 1516-1517
    • Risch, N.1    Merikangas, K.2
  • 54
    • 0000667226 scopus 로고
    • Morphological evidence concerning the B genome in wheat
    • Sarkar, P., and G. L. Stebbins, 1956 Morphological evidence concerning the B genome in wheat. Am. J. Bot. 43: 1-8.
    • (1956) Am. J. Bot. , vol.43 , pp. 1-8
    • Sarkar, P.1    Stebbins, G.L.2
  • 56
    • 85090878417 scopus 로고    scopus 로고
    • LDheatmap: an R function for graphical display of pairwise linkage disequilibrium between single nucleotide polymorphisms
    • Shin, J. H., S. Blay, B. McNeney, and J. Graham, 2006 LDheatmap: an R function for graphical display of pairwise linkage disequilibrium between single nucleotide polymorphisms. J. Stat. Softw. 16: 1-9.
    • (2006) J. Stat. Softw. , vol.16 , pp. 1-9
    • Shin, J.H.1    Blay, S.2    McNeney, B.3    Graham, J.4
  • 57
    • 84872789979 scopus 로고    scopus 로고
    • An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping
    • Sonah, H., M. Bastien, E. Iquira, A. Tardivel, G. Legare et al., 2013 An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8: e54603.
    • (2013) PLoS ONE , vol.8
    • Sonah, H.1    Bastien, M.2    Iquira, E.3    Tardivel, A.4    Legare, G.5
  • 58
    • 0027133066 scopus 로고
    • Mapping polygenes
    • Tanksley, S. D., 1993 Mapping polygenes. Annu. Rev. Genet. 27: 205-233.
    • (1993) Annu. Rev. Genet. , vol.27 , pp. 205-233
    • Tanksley, S.D.1
  • 61
    • 0347361672 scopus 로고    scopus 로고
    • Theoretical basis of the Beavis effect
    • Xu, S., 2003 Theoretical basis of the Beavis effect. Genetics 165: 2259-2268.
    • (2003) Genetics , vol.165 , pp. 2259-2268
    • Xu, S.1
  • 62
    • 84866330869 scopus 로고    scopus 로고
    • Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis
    • Yu, L. X., A. Morgounov, R. Wanyera, M. Keser, S. K. Singh et al., 2012 Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis. Theor. Appl. Genet. 125: 749-758.
    • (2012) Theor. Appl. Genet. , vol.125 , pp. 749-758
    • Yu, L.X.1    Morgounov, A.2    Wanyera, R.3    Keser, M.4    Singh, S.K.5


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