Genomic breeding value prediction and QTL mapping of QTLMAS2010 data using Bayesian Methods

BMC Proceedings

Table 1 Prediction accuracy of GEBV, correlation of GEBV with TBV, correlation of GEBV with genotypic value (g), regression coefficient of phenotype (y) on GEBV, regression coefficient of TBV on GEBV, and regression coefficient of genotypic value on GEBV.

Methods	Correlation of GEBV with			Regression coefficient on GEBV of
	y*¹	TBV	g	y	TBV	g
P-BLUP	0.545	0.410	0.538	1.156	1.003	1.005
G-BLUP
No Poly	0.746	0.610	0.753	1.006	0.949	0.895
Poly	0.737	0.597	0.752	0.961	0.898	0.863
BayesB, π = 0.75
No Poly	0.781	0.632	0.776	1.018	0.950	0.892
Poly	0.778	0.628	0.783	0.984	0.916	0.873
BayesB, π = 0.95
No Poly	0.788	0.640	0.787	1.023	0.960	0.901
Poly	0.784	0.634	0.793	0.983	0.916	0.875
BayesB, π = 0.99
No Poly	0.793	0.646	0.795	1.031	0.967	0.909
Poly	0.790	0.636	0.797	0.981	0.911	0.872
BayesCπ
No Poly	0.796	0.650	0.800	1.011	0.952	0.895
Poly	0.796	0.642	0.804	0.989	0.921	0.880
BayesCπ gen 5 ²
No Poly	–	0.679	0.894	–	0.959	0.965

Results are based on training on the first three generations and validation on generation 4 using P-BLUP, G-BLUP, BayesB with different π's, and BayesCπ, and without (No Poly) and with (Poly) polygenic effects.
¹Calculated as correlation of phenotype (y) with GEBV, divided by the square root of estimated heritability.
²Training on the first 4 generations and predicting generation 5.

ISSN: 1753-6561