Impact of kinship matrices on genetic gain and inbreeding with optimum contribution selection in a genomic dairy cattle breeding program

Table 2 Rates of inbreeding based on drift and homozygosity at neutral loci, QTL and marker loci

Scenario	\({\Delta F}_{drift}\) (%)			\({\Delta F}_{hom}\) (%)			\({F}_{hom}-{F}_{drift}\) (%)
Scenario	Neutral	QTL	Markers	Neutral	QTL	Markers	Neutral	QTL	Markers
VR1 Base	0.656^a	0.945^a	0.654^a	0.427^a	0.524^a	0.414^a	− 1.8	− 4.4	− 2.4
VR1 Old	0.640^a	0.926^a	0.639^a	0.453^a	0.564^ad	0.464^b	− 1.3	− 3.7	− 1.1
VR2 Base	0.666^a	0.955^a	0.663^a	0.463^a	0.605^b	0.484^b	− 1.1	− 2.9	− 0.7
VR1 All	0.750^b	1.053^b	0.749^b	0.546^b	0.702^c	0.557^c	− 2.4	− 4.2	− 2.1
VR2 All	0.795^c	1.108^c	0.797^c	0.641^c	0.721^c	0.612^d	− 1.2	− 4.8	− 1.8
VR1 0.5	0.881^d	1.205^d	0.890^d	0.504^d	0.591^bd	0.485^b	− 7.0	− 10.4	− 7.6
VR1 Current	0.950^e	1.277^e	0.954^e	0.676^cd	0.849^ef	0.729^e	− 2.4	− 4.1	− 2.2
VR2 Current	0.945^e	1.258^ef	0.944^e	0.734^e	0.877^e	0.742^e	− 3.4	− 5.7	− 2.7
Pedigree	0.928^e	1.244^f	0.922^f	0.683^d	0.835^f	0.695^f	− 3.2	− 5.0	− 2.5

Values are in percentages. Values in the same column with different superscript letters are significantly different (P < 0.05) while values is the same column that share a superscript letter are not significantly different
\({\Delta F}_{hom}\): rate of increase of average \({F}_{hom}\) at neutral, QTL and marker loci; \({\Delta F}_{drift}\): rate of increase of average \({F}_{drift}\) at neutral, QTL and marker loci; \({F}_{hom}-{F}_{drift}\): difference between \({F}_{hom}\) and \({F}_{drift}\) at neutral, QTL and marker loci in the last generation of the simulation

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