Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle

BMC Genomics

Table 2 Estimates^a of true inbreeding (F_TRUE), inbreeding derived from runs of homozygosity (F_ROH), inbreeding estimated from the genomic relationship matrix using known base allele frequencies (F_{GRM_Base}) or an allele frequency of 0.5 (F_{GRM_Fixed}) in simulated populations with uniform base allele frequencies (ranging from 0 to 0.5)

	Phenotype selection			Random selection			GEBV selection^c			BLUP-EBV selection^d
Generation	10	30	60	10	30	60	10	30	60	10	30	60
F_TRUE	0.024	0.099	0.209	0.014	0.046	0.092	0.035	0.173	0.411	0.058	0.252	0.554
F_ROH^b	0.026	0.102	0.214	0.017	0.049	0.095	0.038	0.177	0.418	0.060	0.256	0.561
F_{GRM_Fixed}	0.293	0.344	0.422	0.030	0.320	0.350	0.291	0.387	0.562	0.293	0.433	0.661
F_{GRM_Base}	0.030	0.111	0.224	0.018	0.053	0.101	0.045	0.192	0.435	0.074	0.283	0.593

^aStandard error for all estimates ranged from 0.001 to 0.0008
^bF_ROHbased on SNP1101 (minimum homozygosity 20 SNP, genotype error rate 0.001)
^cSelection based on genomic estimated breeding value
^dSelection based on best linear unbiased prediction estimated breeding value

ISSN: 1471-2164