Genome-wide prediction of traits with different genetic architecture through efficient variable selection

Genetics

Volumn 195, Issue 2, 2013, Pages 573-587

  Wimmer, Valentin ^a   Lehermeier, Christina ^a   Albrecht, Theresa ^a,b   Auinger, Hans Jürgen ^a   Wang, Yu ^a   Schön, Chris Carolin ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b Bavarian State Research Center for Agriculture   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; BAYESB; COMPUTER SIMULATION; CONTROLLED STUDY; EXPERIMENTAL STUDY; FLOWERING; FRIGIDA GENE; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ARCHITECTURE; HERITABILITY; LARGE SCALE PRODUCTION; LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATOR; NONHUMAN; PHENOTYPE; PLANT BREEDING; PREDICTION; PREDICTOR VARIABLE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RICE; RIDGE REGRESSION BEST LINEAR UNBIASED PREDICTION; SAMPLE SIZE; STATISTICAL ANALYSIS; TRITICUM AESTIVUM;

COMPLEX TRAITS; GENETIC ARCHITECTURE; GENOME-BASED PREDICTION; GENPRED; PLANT BREEDING POPULATIONS; SHARED DATA RESOURCES; VARIABLE SELECTION;

ARABIDOPSIS; BREEDING; COMPUTER SIMULATION; GENOME, PLANT; LINEAR MODELS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; ORYZA SATIVA; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC; TRITICUM;

EID: 84884945790     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.150078     Document Type: Article

References (41)

1. Albrecht, T., V. Wimmer, H.-J. Auinger, M. Erbe, C. Knaak et al., 2011 Genome-based prediction of testcross values in maize. Theor. Appl. Genet. 123: 339-350.
2. Atwell, S., Y. Huang, B. Vilhjálmsson, G. Willems, M. Horton et al., 2010 Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
3. Bates, D., and M. Maechler, 2012 Matrix: sparse and dense matrix classes and methods. R Package Version 1.0-6.
4. Browning, B. L., and S. R. Browning, 2009 A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 846: 210-223.
5. Butts, C. T., 2008 Network: a package for managing relational data in R. J. Stat. Softw. 24: 1-36.
6. Clark, S., J. Hickey, and J. van der Werf, 2011 Different models of genetic variation and their effect on genomic evaluation. Genet. Sel. Evol. 43: 18.
7. Daetwyler, H. D., R. Pong-Wong, B. Villanueva, and J. A. Woolliams, 2010 The impact of genetic architecture on genome-wide evaluation methods. Genetics 185: 1021-1031.
8. de los Campos, G., D. Gianola, and D. B. Allison, 2010 Predicting genetic predisposition in humans: the promise of whole-genome markers. Nat. Rev. Genet. 11: 880-886.
9. de los Campos, G., J. M. Hickey, R. Pong-Wong, H. D. Daetwyler, and M. P. L. Calus, 2013 Whole genome regression and prediction methods applied to plant and animal breeding. Genetics 193: 327-345.
10. Donoho, D. L., and V. Stodden, 2006 Breakdown point of model selection when the number of variables exceeds the number of observations, pp. 1916-1921 in Proceedings of the International Joint Conference on Neural Networks. Vancouver, British Columbia.
11. Fernando, R., and D. Garrick, 2009 GenSel-User Manual of Genomic Selection Related Analyses, Iowa State University, Ames, Iowa.
12. Friedman, J., T. Hastie, and R. Tibshirani, 2010 Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 30: 1-22.
13. Gilmour, A., B. Gogel, B. Cullis, and R. Thompson, 2009 ASReml User Guide Release 3.0. VSN International, Hemel Hempstead, UK.
14. Habier, D., R. L. Fernando, and J. C. M. Dekkers, 2007 The impact of genetic relationship information on genome-assisted breeding values. Genetics 177: 2389-2397.
15. Habier, D., J. Tetens, F. Seefried, P. Lichtner, and G. Thaller, 2010 The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Sel. Evol. 42: 5.
16. Habier, D., R. L. Fernando, K. Kizilkaya, and D. J. Garrick, 2011 Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics 12: 186.
17. Hastie, T., R. Tibshirani, and J. Friedman, 2009 The Elements of Statistical Learning: Data Mining, Inference, and Prediction (Springer Series in Statistics, Ed. 2). Springer-Verlag, Stanford, CA.
18. Hayes, B. J., J. Pryce, A. J. Chamberlain, P. J. Bowman, and M. E. Goddard, 2010 Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet. 6: e1001139.
19. Heslot, N., H.-P. Yang, M. E. Sorrells, and J.-L. Jannink, 2012 Genomic selection in plant breeding: a comparison of models. Crop Sci. 52: 146-160.
20. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 6: 226-231.
21. Hofheinz, N., D. Borchardt, K. Weissleder, and M. Frisch, 2012 Genome-based prediction of test cross performance in two subsequent breeding cycles. Theor. Appl. Genet. 125: 1639-1645.
22. Ishwaran, H., and J. S. Rao, 2011 Generalized ridge regression: geometry and computational solutions when p is larger than n. Technical report. Cleveland Clinic and University of Miami, Miami.
23. Legarra, A., C. Robert-Granie, E. Manfredi, and J. Elsen, 2008 Performance of genomic selection in mice. Genetics 180: 611-618.
24. Meuwissen, T. H. E., and M. E. Goddard, 2010 Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185: 623-631.
25. Meuwissen, T. H. E., B. J. Hayes, and M. E. Goddard, 2001 Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
26. Ober, U., J. F. Ayroles, E. A. Stone, S. Richards, D. Zhu et al., 2012 Using whole genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet. 8: e1002685.
27. Pepe, M. S., 2004 The Statistical Evaluation of Medical Tests for Classification and Prediction. Oxford University Press, New York.
28. Pérez-Rodríguez, P., D. Gianola, J. M. González-Camacho, J. Crossa, Y. Manès et al., 2012 Comparison between linear and non-parametric regression models for genome-enabled prediction in wheat. G3 2: 1595-1605.
29. Poland, J., J. Endelman, J. Dawson, J. Rutkoski, S. Wu et al., 2012 Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genet. 5: 103-113.
30. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira et al., 2007 Plink: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81: 559-575.
31. R Development Core Team, 2012 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
32. Riedelsheimer, C., F. Technow, and A. Melchinger, 2012 Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines. BMC Genomics 13: 452.
33. Schön, C.-C., H. F. Utz, S. Groh, B. Truberg, S. Openshaw et al., 2004 Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167: 485-498.
34. Stodden, V., 2006 Model selection when the number of variables exceeds the number of observations. Ph.D. Thesis, Department of Statistics, Stanford University, Stanford, CA.
35. Tibshirani, R., 1996 Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. B 58: 267-288.
36. Wimmer, V., T. Albrecht, H.-J. Auinger, and C.-C. Schön, 2012 synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics 28: 2086-2087.
37. Yu, J., X. Li, C. Zhu, C. T. Yeh, W. Wu et al., 2012 Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res. 12: 2436-2444.
38. Zhang, Z., J. Liu, X. Ding, P. Bijma, D.-J. De Koning et al., 2010 Best linear unbiased prediction of genomic breeding values using a trait-specific marker-derived relationship matrix. PLoS ONE 5: 0012648.
39. Zhao, K., C.-W. Tung, G. C. Eizenga, M. H. Wright, M. L. Ali et al., 2011 Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2: 467.
40. Zhong, S., J. C. M. Dekkers, R. L. Fernando, and J.-L. Jannink, 2009 Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182: 355-364.
41. Zou, H., and T. Hastie, 2005 Regularization and variable selection via the elastic net. J. R. Stat. Soc. B 67: 301-320.