Effect of Prior Distributions on Accuracy of Genomic Breeding Values for Two Dairy Traits

Figures & data

Figure 1. Absolute values of SNP effects in the simulated dataset. The crossed squares indicate (absolute) simulated true QTL effects and the triangles indicate SNP effects for BayesA (a), B-LASSOgamma (b), B-LASSObeta (c), and BGR (d). On the x-axis, SNP are ordered by position from chromosome 1 to 6.

Figure 2. Absolute values of SNP effects in the real dataset for fat percentage. Mean posterior estimates of SNP effects (y-axis) for the 39.048 SNP considered (x-axis, displayed ordered by position from BTA1 to BTA29) obtained with BayesA (a), B-LASSOgamma (b), B-LASSObeta (c), and BGR (d).

Figure 3. Absolute values of SNP effects in the real dataset for protein yield. Mean posterior estimates of SNP effects (y-axis) for the 39.048 SNP considered (x-axis, displayed ordered by position from BTA1 to BTA29) obtained with BayesA (a), B-LASSOgamm a (b), B-LASSObeta (c), and BGR (d).

Table 1. Absolute SNP effects in simulated QTL regions with high effect.

Chr.^°	Position, cm	β^#	BayesA		B-LASSO gamma		B-LASSO beta		BGR
			ĝ ^§	Dif^∧	ĝ ^§	Dif^∧	ĝ ^§	Dif^∧	ĝ ^§	Dif^∧
1	20.00	0.62	0.60	−0.02	0.09	−0.53	0.08	−0.54	0.02	−0.60
1	40.00	0.56	0.12	−0.44	0.02	−0.54	0.03	−0.53	0.01	−0.55
1	77.23	0.37	0.38	0.01	0.04	−0.33	0.04	−0.33	0.01	−0.36
2	27.41	0.35	0.23	−0.12	0.03	−0.32	0.04	−0.31	0.01	−0.34
2	30.00	0.33	0.01	−0.32	0.02	−0.31	0.01	−0.32	0.01	−0.32
2	48.62	0.37	0.31	−0.06	0.05	−0.32	0.05	−0.32	0.02	−0.35
2	74.91	0.50	0.01	−0.49	0.02	−0.48	0.01	−0.49	0.01	−0.49
3	14.91	0.30	0.03	−0.27	0.02	−0.28	0.02	−0.28	0.01	−0.29
3	60.00	0.68	0.26	−0.42	0.03	−0.65	0.03	−0.65	0.01	−0.67
4	3.21	0.61	0.37	−0.24	0.12	−0.49	0.13	−0.48	0.02	−0.59
4	36.93	0.34	0.02	−0.32	0.02	−0.32	0.01	−0.33	0.01	−0.33
4	76.06	0.58	0.50	−0.08	0.07	−0.51	0.07	−0.51	0.02	−0.56
4	96.49	0.29	0.06	−0.23	0.04	−0.25	0.03	−0.26	0.01	−0.28
5	5.15	0.18	0.05	−0.13	0.02	−0.16	0.02	−0.16	0.01	−0.17
5	93.50	0.75	0.65	−0.10	0.25	−0.50	0.24	−0.51	0.03	−0.72

°Chromosomes where QTL with large effect were simulated; no QTL was simulated on chromosome 6.

^#Absolute (true) value of major QTL effects.

^§Mean posteriors of SNP effects in the region of QTL with moderate to large effects.

Difference between true QTL effect and mean posterior of SNP effect in the region of the QTL.

Table 2. Accuracies, regression coefficients and regularization parameters obtained in the simulated dataset.

	BayesA	B-LASSO gamma	B-LASSO beta	BGR
r(TBV,DGV)^°	0.87	0.77	0.77	0.74
r(Phe,DGV)^#	0.432	0.392	0.390	0.373
b(TBV,DGV)^§	1.009	0.867	0.859	1.185
λ^∧	-	98.79 (4.60)	97.45 (4.11)	-

°Accuracy in validation population, obtained as correlation between true breeding values and direct genomic breeding values.

^#Accuracy in validation population, obtained as correlation between precorrected phenotypes and direct genomic breeding values.

^§Regression coefficients of true breeding values on direct genomic breeding values.

∧Posterior mean (and standard deviation) of the regularization parameter for both Bayesian-LASSO methods.

Table 3. Accuracies, regression coefficients and regularization parameters obtained in the real dataset for fat percentage.

	BayesA	B-LASSO gamma	B-LASSO beta	BGR
r(ABV,DGV)^°	0.75	0.71	0.71	0.59
b(ABV,DGV)^#	0.943	1.110	1.108	1.395
λ^§	-	100.48(4.09)	70.04 (6.50)	-

°Accuracy in validation population as correlation between Australian breeding values and direct genomic breeding values.

^#Regression coefficients of Australian breeding values on direct genomic breeding values.

^§Posterior mean (and standard deviation) of the regularization parameter for both Bayesian-LASSO methods.

Table 4. Accuracies, regression coefficients and regularization parameters obtained in the real dataset for protein yield.

	BayesA	B-LASSO gamma	B-LASSO beta	BGR
r(ABV,DGV)^°	0.52	0.48	0.48	0.47
b(ABV,DGV)^#	1.112	1.327	1.241	1.474
λ^§	128.72 (15.59)	108.47 (11.57)	-	-

°Accuracy in validation population as correlation between Australian breeding values and direct genomic breeding values.

^#Regression coefficients of Australian breeding values on direct genomic breeding values.

^§Posterior mean (and standard deviation) of the regularization parameter for both Bayesian-LASSO methods.