Simultaneous QTL detection and genomic breeding value estimation using high density SNP chips

BMC Proceedings

Table 1 Evaluation of predicted breeding values (EBV) at point 600 for the animals without phenotypic data

	BLUP	SNP1	SNP2	SNP3	IBS2	IBS5 IBD	14 SNP
BLUP	1
SNP1	0.71	1
SNP2	0.76	0.93	1
SNP3	0.75	0.93	1	1
IBS2	0.74	0.93	0.99	0.99	1
IBS5	0.75	0.94	0.99	0.99	0.99	1
IBD	0.75	0.95	0.98	0.98	0.98	0.98 1
14 SNP	0.72	0.93	0.99	0.99	0.99	0.98 0.97	1
	Association EBV with true breeding value
Variance EBV	10.8	25.0	18.0	17.9	18.3	19.6 19.0	20.2
Accuracy	0.65	0.91	0.93	0.93	0.93	0.93 0.93	0.93
Mean sq. error	14.7	4.4	3.8	3.7	3.5	3.5 3.5	3.5
Regression
coefficient	0.99	0.92	1.10	1.10	1.10	1.06 1.08	1.04

Correlations between breeding values predicted using the additive genetic relationship matrix (BLUP), and haplotype defined as single SNP (effects sampled from 1, 2 or 3 distributions), IBD haplotypes, and IBS haplotypes (combing 2 or 5 SNP), and association with simulated true breeding value.

ISSN: 1753-6561