High density marker panels, SNPs prioritizing and accuracy of genomic selection

BMC Genomic Data

Table 4 Number of selected SNPs, number of tagged QTL, percentage of genetic variance explained, and accuracies of genomic and phenotype prediction under different π values, sampling distribution for the QTL effects and density of the marker panel using BayesB method. Standard errors of accuracies are listed between parentheses

	(1-π) =0.90		(1-π) =0.95		(1-π) =0.98		(1-π) =0.99
	Gamma¹	Predefined²	Gamma	Predefined	Gamma	Predefined	Gamma	Predefined
200 K marker density
# SNP	20 K	20 K	10 K	10 K	4 K	4 K	2 K	2 K
Tagged QTL³	78	98	63	97	54	94	48	91
% GV⁴	89.31	98.16	86.43	97.88	84.30	95.76	83.88	93.20
Acc_P⁵	0.473	0.463	0.478	0.471	0.489	0.487	0.499	0.500
	(0.018)	(0.009)	(0.018)	(0.009)	(0.018)	(0.008)	(0.018)	(0.007)
Acc_G⁶	0.797	0.770	0.807	0.785	0.827	0.810	0.845	0.833
	(0.017)	(0.008)	(0.017)	(0.007)	(0.018)	(0.007)	(0.018)	(0.005)
400 K marker density
# SNP	40K	40K	20 K	20 K	8 K	8 K	4 K	4 K
Tagged QTL	86	99	75	98	59	97	53	96
% GV	92.36	98.46	91.88	98.16	91.20	97.78	91.03	96.69
Acc_P	0.465	0.450	0.470	0.457	0.478	0.469	0.488	0.481
	(0.015)	(0.018)	(0.015)	(0.018)	(0.014)	(0.018)	(0.013)	(0.019)
Acc_G	0.790	0.756	0.799	0.767	0.813	0.787	0.829	0.807
	(0.019)	(0.013)	(0.017)	(0.013)	(0.016)	(0.014)	(0.015)	(0.014)

¹ QTL effects sampled from a Gamma distribution, ²QTL effects pre-defined to explain at least 0.5% of genetic variance (GV), ³QTL with r² > 0.7 with at least one selected SNP, ⁴ GV = Genetic Variance, ⁵ accuracy of phenotype prediction, ⁶accuracy of genomic prediction

ISSN: 2730-6844