Genomic prediction of disease occurrence using producer-recorded health data: a comparison of methods

Table 2 Single-trait model variance component estimates (standard deviation)

	Mastitis
	Data without daughter restrictions				Data with daughter restrictions
	Pedigree-based analysis		Single-step analysis		Pedigree-based analysis		Single-step analysis
	Full data	Training data	Full data	Training data	Full data	Training data	Full data	Training data
\({\sigma _{s}^{2}}\)	0.02 (0.004)	0.03 (0.004)	0.04 (0.006)	0.05 (0.007)	0.02 (0.006)	0.02 (0.006)	0.04 (0.01)	0.02 (0.008)
\({\sigma _{h}^{2}}\)	0.49 (0.03)	0.46 (0.03)	0.49 (0.02)	0.46 (0.03)	0.43 (0.03)	0.41 (0.04)	0.43 (0.03)	0.41 (0.04)
\({\sigma _{e}^{2}}\)	1.0 (0.006)	1.0 (0.007)	1.0 (0.006)	1.0 (0.007)	1.0 (0.01)	1.0 (0.01)	1.0 (0.01)	1.0 (0.01)
h ²	0.10 (0.01)	0.12 (0.01)	0.10 (0.02)	0.12 (0.02)	0.05 (0.02)	0.05 (0.02)	0.11 (0.03)	0.06 (0.02)
	Somatic Cell Score
	Pedigree-based analysis		Single-step analysis		Pedigree-based analysis		Single-step analysis
	Full data	Training data	Full data	Training data	Full data	Training data	Full data	Training data
\({\sigma _{s}^{2}}\)	0.04 (0.004)	0.04 (0.004)	0.07 (0.006)	0.07 (0.006)	0.05 (0.008)	0.05 (0.008)	0.10 (0.02)	0.10 (0.02)
\({\sigma _{h}^{2}}\)	0.53 (0.02)	0.53 (0.02)	0.53 (0.02)	0.52 (0.02)	0.52 (0.02)	0.50 (0.03)	0.52 (0.02)	0.50 (0.03)
\({\sigma _{e}^{2}}\)	1.64 (0.008)	1.64 (0.008)	1.63 (0.008)	1.60 (0.008)	1.62 (0.01)	1.62 (0.02)	1.62 (0.01)	1.62 (0.02)
h ²	0.08 (0.01)	0.08 (0.01)	0.13 (0.01)	0.13 (0.01)	0.08 (0.01)	0.08 (0.01)	0.18 (0.03)	0.18 (0.03)

Estimated variance components include sire variance (σ s2), herdyear variance (σ h2), residual variance (σ e2) and heritability (h ²) for full and training datasets from pedigree-based and single-step analyses of mastitis and somatic cell score.

ISSN: 1297-9686