Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers

Table 3 Summary of accuracy of DGV using low-density assays derived by PLSR

Test set	SNP selection	Number of SNP
		5,000	3,000	1,000	500	300	100
Bulls		Trait-specific assay
		89	85	84	78	72	59
		Common assay of evenly spaced SNP
	ASI	88	86	68	67	65	32
	APR	92	86	68	67	65	32
	MAF	86	80	61	62	58	40
Cows		Trait-specific assay
		98	96	88	80	80	72
		Common assay of evenly spaced SNP
	ASI	94	92	85	75	69	47
	APR	92	90	79	77	69	52
	MAF	94	93	78	79	57	42

Accuracy of prediction is shown as percentage of the accuracy obtained with 42,576 SNP, averaged over nine traits for bulls and four traits for cows.

ISSN: 1297-9686