Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle

Table 1 Estimates of genetic parameters

Trait	Genotype data	Method	σ ²_g	h ²	b ^(a)	r ² ^(b)
SCS	Pedigree	BLUP	20.22	0.97	1.00	0.33
	BovineHD	GBLUP	16.97	0.90	0.96	0.52
	BovineHD	BSSVS	18.55	0.95	0.99	0.52
	ImputedHD	GBLUP	17.41	0.93	1.00	0.50
	ImputedHD	BSSVS	18.37	0.98	1.05	0.51
	Sequence	GBLUP	17.09	0.93	1.03	0.49
	Sequence	BSSVS	18.82	0.98	1.04	0.50
IFL	Pedigree	BLUP	19.60	1.00	0.92	0.27
	BovineHD	GBLUP	15.90	0.94	0.83	0.39
	BovineHD	BSSVS	18.01	0.99	0.92	0.40
	ImputedHD	GBLUP	16.29	0.95	0.86	0.37
	ImputedHD	BSSVS	17.20	1.00	0.97	0.39
	Sequence	GBLUP	16.13	0.96	0.88	0.37
	Sequence	BSSVS	17.71	1.00	0.95	0.39
PY	Pedigree	BLUP	341.05	1.00	0.82	0.26
	BovineHD	GBLUP	295.05	0.94	0.86	0.47
	BovineHD	BSSVS	306.53	0.99	0.89	0.48
	ImputedHD	GBLUP	307.33	0.97	0.89	0.44
	ImputedHD	BSSVS	285.36	1.00	0.95	0.45
	Sequence	GBLUP	300.68	0.98	0.92	0.44
	Sequence	BSSVS	293.73	1.00	0.95	0.45

Estimates of additive genetic variance (σ ²_g ), heritability (h ²), regression coefficient (b), and prediction reliability (r ²) for somatic cell score (SCS), interval between first and last insemination (IFL), and protein yield (PY) using four types of data and two prediction methods. ^aStandard error of the regression coefficient ranged from 0.02 to 0.03; ^bstandard error of the prediction reliability was 0.02

ISSN: 1297-9686