On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL

Table 2 Correlation between GEBV and (D)YD^a for kg milk, kg fat, kg protein, fat percentage and protein percentage using within-breed (WB) and across-breed (AB) GBLUP, and across-breed Bayes GC predictions

	N^b	GBLUP(WB)	GBLUP(AB)	BayesGC	Accuracy (D)YD
kg milk (variance due to SNPs 15%; posterior probability = 0.00048) ^c
Holstein bulls	826	0.713	0.714	0.729	0.970
Jersey bulls	221	0.617	0.643	0.674	0.964
Australian Red cows	1579	–	0.23	0.263	0.469
kg fat (variance due to SNPs 25%; posterior probability = 0.00049) ^c
Holstein bulls	826	0.655	0.658	0.669	0.954
Jersey bulls	221	0.699	0.683	0.688	0.949
Australian Red cows	1579	–	0.229	0.281	0.389
kg protein (variance due to SNPs 24%; posterior probability = 0.00050) ^c
Holstein bulls	826	0.672	0.67	0.677	0.954
Jersey bulls	221	0.716	0.711	0.724	0.949
Australian Red cows	1579	–	0.168	0.201	0.383
Fat % (variance due to SNPs 13%; posterior probability = 0.00047) ^c
Holstein bulls	826	0.818	0.794	0.797	0.975
Jersey bulls	221	0.631	0.649	0.681	0.973
Australian Red cows	1579	–	0.245	0.267	0.522
Protein % (variance due to SNPs 8%; posterior probability = 0.00047) ^c
Holstein bulls	826	0.87	0.87	0.875	0.982
Jersey bulls	221	0.793	0.819	0.835	0.979
Australian Red cows	1579	–	0.179	0.343	0.574

^aDYD: daughter yield deviation for Holstein and Jersey bulls; YD: yield deviation for Australian Red Cows
^bNumber of validation animals
^cThe fraction of the genetic variance explained by SNPs is indicated together with the average fraction of the SNPs fitted to explain this variance (posterior prob), and the accuracy of the (D)YD used for validation

ISSN: 1297-9686