Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein–Friesian cattle

Table 4 Phenotypic variance explained (h²) in 2287 validation animals for protein yield (PY), somatic cell score (SCS) and interval first –last insemination (IFL)

Trait	Selection criteria	ISQ	HD	50k	ISQ	HD	50k	ISQ	HD	50k
Trait	Selection criteria	Selected set of variants (GRM)			Complementary set of variants (GRMc)			Sum of GRM and GRMc
PY	All variants	0.83	0.98	0.70		0.00	0.12	0.83	0.98	0.82
	−log10(p) > 3	0.19	0.15	0.09	0.61	0.65	0.73	0.80	0.80	0.82
	−log10(p) > 5	0.10	0.04	0.03	0.74	0.79	0.80	0.84	0.83	0.83
	COJO3	0.11			0.70			0.81
	COJO5	0.10			0.71			0.81
	COJO5LD	0.08			0.73			0.82
	COJO#100	0.09			0.72			0.82
SCS	All variants	0.87	0.87	0.48		0.00	0.38	0.87	0.87	0.86
	−log10(p) > 3	0.22	0.15	0.05	0.60	0.68	0.80	0.82	0.83	0.85
	−log10(p) > 5	0.24	0.03	0.01	0.64	0.84	0.85	0.88	0.87	0.86
	COJO3	0.14			0.68			0.81
	COJO5	0.14			0.66			0.80
	COJO5LD	0.05			0.79			0.84
	COJO#100	0.08			0.76			0.83
IFL	All variants	0.72	0.85	0.50		0.00	0.21	0.72	0.85	0.70
	−log10(p) > 3	0.20	0.12	0.05	0.51	0.57	0.64	0.70	0.69	0.69
	−log10(p) > 5	0.11	0.03	0.03	0.63	0.69	0.70	0.73	0.72	0.72
	COJO3	0.11			0.57			0.67
	COJO5	0.12			0.57			0.69
	COJO5LD	0.07			0.64			0.71
	COJO#100	0.08			0.64			0.71

COJO analysis with −log10(p) > 3 (COJO3) or −log10(p) > 5 (COJO5); ISQ are all imputed sequence variants, HD and 50k are the SNPs on the common HD and 50k panels
Variances are estimated fitting \({\mathbf{GRM}}\) and \({\mathbf{GRMc}}\) together in one model where \({\mathbf{GRM}}\) were based on the selected set of variants and \({\mathbf{GRMc}}\) on the complementary variants. Set of variants that were selected using GWAS results on 3469 discovery animals

ISSN: 1297-9686