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

Table 5 Prediction accuracy in 2287 validation animals, and the intercept and slope for the regression of phenotype on the breeding value estimated using GRM with different selected sets of variants 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	Accuracy			Intercept			Slope
PY	All variants	0.68	0.68	0.68	−0.6	−0.6	−0.7	0.90	0.90	0.89
	−log10(p) > 3	0.58	0.56	0.42	2.3	3.6	6.9	0.73	0.65	0.57
	−log10(p) > 5	0.39	0.30	0.28	7.2	8.7	9.4	0.54	0.51	0.71
	COJO3	0.40			7.2			0.45
	COJO5	0.38			7.7			0.41
	COJO5LD	0.33			8.1			0.51
	COJO#100	0.34			7.2			0.47
SCS	All variants	0.70	0.71	0.70	100	100	100	1.02	1.03	1.03
	−log10(p) > 3	0.63	0.55	0.36	100	100	101	0.82	0.79	0.70
	−log10(p) > 5	0.40	0.22	0.11	100	101	101	0.79	0.66	0.57
	COJO3	0.48			100			0.64
	COJO5	0.48			100			0.60
	COJO5LD	0.35			100			0.68
	COJO#100	0.39			100			0.66
IFL	All variants	0.60	0.60	0.60	99	99	99	0.88	0.87	0.86
	−log10(p) > 3	0.51	0.45	0.31	99	99	99	0.70	0.62	0.52
	−log10(p) > 5	0.27	0.16	0.10	99	98	98	0.47	0.51	0.77
	COJO3	0.38			99			0.45
	COJO5	0.35			99			0.41
	COJO5LD	0.30			99			0.52
	COJO#100	0.32			99			0.45

ISQ are all imputed sequence variants, HD and 50k are the SNPs on the common HD and 50k panels. Set of variants that were selected using GWAS and subsequently trained in 3469 discovery animals

ISSN: 1297-9686