Bayesian methods for estimating GEBVs of threshold traits

Heredity

Volumn 110, Issue 3, 2013, Pages 213-219

  Wang, C L ^a,b   Ding, X D ^a   Wang, J Y ^a   Liu, J F ^a   Fu, W X ^a   Zhang, Z ^a   Yin, Z J ^a   Zhang, Q ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b RICE RESEARCH INSTITUTE   (China)

Author keywords

Bayesian methods; genomic selection; MCMC; threshold traits

Indexed keywords

ALGORITHM; BAYESIAN ANALYSIS; COMPUTER SIMULATION; ESTIMATION METHOD; GENOMICS; MARKOV CHAIN; NUMERICAL MODEL; THRESHOLD;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BREEDING; CATTLE; COMPUTER SIMULATION; FEMALE; GENETIC SELECTION; GENOTYPE; HUMAN; MALE; MONTE CARLO METHOD; PHENOTYPE; PROBABILITY; QUANTITATIVE TRAIT; STATISTICS;

ANIMALS; BAYES THEOREM; BREEDING; CATTLE; COMPUTER SIMULATION; FEMALE; GENOTYPE; HUMANS; MALE; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE; SELECTION, GENETIC;

EID: 84873991295     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.65     Document Type: Article

References (31)

1. Albert JH, Chib S (1993). Bayesian analysis of binary and polychotomous response data. J Am Stat Assoc 88: 669-679.
2. Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA (2010). The impact of genetic architecture on genome-wide evaluation methods. Genetics 185: 1021-1031.
3. Dempster ER, Lerner IM (1950). Heritability of threshold characters. Genetics 35: 212-236.
4. Falconer DS, Mackay TFC (1996). Introduction to Quantitative Genetics, 4th edn. Longman: Essex, UK.
5. Friedman J, Hastie T, Tibshirani R (2010). Regularization paths for generalized linear models via coordinate descent. J Stat Softw 33: 1-22.
6. George EI, McCulloch RE (1993). Variable selection via Gibbs sampling. J Am Stat Association 91: 883-904.
7. Gianola D (1982). Theory and analysis of threshold characters. J Anim Sci 54: 1079-1096.
8. Gianola D, Foulicy JL (1983). Sire evaluation for ordered categorical data with a threshold model. Genet Sel Evol 15: 201-224.
9. Gianola D, Fernando RL, Stella A (2006). Genomic-assisted prediction of genetic value with semiparametric procedures. Genetics 173: 1761-1776.
10. Gilmour AR, Anderson RD, Rae AL (1985). The analysis of binomial data by a generalized linear mixed model. Biometrika 72: 593-599.
11. Goddard ME, Hayes BJ (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10: 381-391.
12. González-Recio O, Forni S (2011). Genome-wide prediction of discrete traits using Bayesian regressions and machine learning. Genet Sel Evol 43: 7.
13. Habier D, Fernando RL, Kizilkaya K, Garrick DJ (2011). Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics 12: 186.
14. Hoerl AE, Kennard RW (1970). Ridge regression: biased estimation for nonorthogonal problems. Techno metrics 12: 55-67.
15. Ishwaran H, Rao JS (2005). Spike and slab variable selection: frequentist and Bayesian strategies. Ann Stat 33: 730-773.
16. Meuwissen THE, Hayes BJ, Goddard ME (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
17. Solberg TR, Sonesson AK, Woolliams JA, Meuwissen THE (2009). Reducing dimensionality for prediction of genome-wide breeding values. Genet Sel Evol 41: 29.
18. Sorensen D, Andersen S, Gianola D, Korsgaard I (1995). Bayesian inference in threshold models using Gibbs sampling. Genet Sel Evol 27: 229-249.
19. Sorensen D, Gianola D (2002). Likelihood, Bayesian and MCMC Methods in Quantitative Genetics. Springer-Verlag: New York.
20. Szydlowski M, Paczyńska P (2011). QTLMAS 2010: simulated dataset. BMC Proc 5(Suppl 3): S3.
21. VanRaden PM (2008). Efficient methods to compute genomic predictions. J Dairy Sci 91: 4414-4423.
22. Villanueva B, Fernández J, García-Cortés LA, Varona L, Daetwyler HD, Toro MA (2011). Accuracy of genome-wide evaluation for disease resistance in aquaculture breeding programs. J Anim Sci 89: 3433-3442.
23. Wang H, Zhang YM, Li X, Masinde GL, Mohan S, Baylink DJ et al. (2005). Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480.
24. Wright S (1934). An analysis of variability in number of digits in an inbred strain of Guinea Pigs. Genetics 19: 506-536.
25. Xu S (2003). Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
26. Xu S (2007). An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63: 513-521.
27. Yi N, George V, Allison DB (2003). Stochastic search variable selection for identifying quantitative trait loci. Genetics 164: 1129-1138.
28. Yi N, Xu S (2008). Bayesian LASSO for quantitative trait loci mapping. Genetics 179: 1045-1055.
29. Zhang Q (2007). Computational Methods in Animal Breeding. Science Press: Beijing.
30. Zhang Z, Liu J, Ding X, Bijma P, de Koning D-J, Qin Z (2010). Best linear unbiased prediction of genomic breeding values using a trait-specific marker-derived relationship matrix. PLoS ONE 5: e12648.
31. Zou H, Hastie T (2005). Regularization and variable selection via the elastic net. J Royal Stat Soc B 67: 301-320.