Inbreeding depression across the genome of Dutch Holstein Friesian dairy cattle

Table 1 Effect of a 1% increase in genome-wide homozygosity (\(b\)), and mean dominance effect per SNP (\(-b/{N}_{SNP}\)), for three models and nine traits

Trait	\({N}_{cows}\)	Model A		Model AD		Model ADR
Trait	\({N}_{cows}\)	\(b\)(SE)	\(-b/{N}_{SNP}\)	\(b\)(SE)	\(-b/{N}_{SNP}\)	\(b\)(SE)	\(-b/{N}_{SNP}\)
MY	38,778	− 99.6 (5.2)	0.1322	− 98.7 (6.1)	0.1310	− 97.8 (6.7)	0.1298
FY	38,778	− 4.10 (0.20)	0.0054	− 4.04 (0.23)	0.0054	− 4.01 (0.27)	0.0053
PY	38,778	− 3.49 (0.17)	0.0046	− 3.45 (0.20)	0.0046	− 3.42 (0.23)	0.0045
CI	34,864	1.11 (0.35)	− 0.0015	1.11 (0.35)	− 0.0015	1.11 (0.38)	− 0.0015
ICF	34,937	0.20 (0.15)	− 0.0003	0.21 (0.16)	− 0.0003	0.21 (0.17)	− 0.0003
IFL	34,937	0.79 (0.30)	− 0.0011	0.79 (0.30)	− 0.0010	0.79 (0.30)	− 0.0010
CR (%)	34,774	− 0.68 (0.19)	9.0E–06	− 0.68 (0.19)	9.0E–06	− 0.68 (0.19)	9.0E–06
SCS150	38,301	1.09 (0.69)	− 0.0015	1.08 (0.70)	− 0.0015	1.09 (0.71)	− 0.0014
SCS400	37,068	2.28 (0.67)	− 0.0030	2.26 (0.70)	− 0.0030	2.26 (0.70)	− 0.0030

Model A, additive model; AD, additive + dominance model; ADR, additive + dominance + ROH model
MY, 305-day milk yield (kg); FY, 305-day fat yield (kg); PY, 305-day protein yield (kg); CI, calving interval (days); ICF, interval calving to first insemination (days); IFL, interval first to last insemination (days); CR: conception rate (%); SCS150 somatic cell score day 5 to 150 (1000 + 100* [log2 of cells/mL]); SCS400: somatic cell score day 151 to 400 (1000 + 100*[log2 of cells/mL])

ISSN: 1297-9686