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

Table 1 Rate of increase in average kinship, genetic gain, loss of genetic variance, and average MAF

Scenario	\(\Delta f\) (%)	\(\Delta G\)	\(\Delta {\sigma }_{A}^{2}\) (%)	\(\Delta {\sigma }_{G}^{2}\) (%)	Relative to Pedigree*				MAF
Scenario	\(\Delta f\) (%)	\(\Delta G\)	\(\Delta {\sigma }_{A}^{2}\) (%)	\(\Delta {\sigma }_{G}^{2}\) (%)	\(\Delta f\)	\(\Delta G\)	\(\Delta {\sigma }_{A}^{2}\)	\(\Delta {\sigma }_{G}^{2}\)	QTL	Neutral
VR1 Base	0.500^a	0.863^a	− 2.5^a	− 2.4^a	0.67	0.96	0.80	0.91	0.201	0.209
VR1 Old	0.510^a	0.865^a	− 2.6^b	− 2.5^a	0.68	0.96	0.84	0.92	0.201	0.210
VR2 Base	0.514^a	0.865^a	− 2.5^a	− 2.4^a	0.69	0.96	0.81	0.91	0.198	0.207
VR1 All	0.606^b	0.892^b	− 2.9^c	− 2.6^b	0.81	0.99	0.94	0.96	0.195	0.206
VR2 All	0.646^c	0.897^bc	− 3.0^c	− 2.6^b	0.87	1.00	0.97	0.97	0.193	0.201
VR1 0.5	0.702^e	0.896^bc	− 2.9^c	− 2.6^b	0.94	1.00	0.95	0.96	0.198	0.208
VR1 Current	0.785^d	0.903^d	− 3.1^d	− 2.7^c	1.05	1.00	1.00	1.01	0.185	0.194
VR2 Current	0.785^d	0.905^d	− 3.1^d	− 2.7^c	1.05	1.01	1.00	1.02	0.184	0.193
Pedigree	0.746^f	0.900^c	− 3.1^d	− 2.7^c	1.00	1.00	1.00	1.00	0.186	0.194

*Values are proportional to those in Pedigree
Values in the same column with different superscript letters are significantly different (P < 0.05) while values in the same column that share a superscript letter are not significantly different
\(\Delta f\): rate of increase of average kinship in percentages; \(\Delta G\): rate of genetic gain expressed in units of additive genetic standard deviations; \(\Delta {\sigma }_{A}^{2}\): rate of loss of additive genetic variance in percentages relative to generation five; \(\Delta {\sigma }_{G}^{2}\): rate of loss of additive genic variance in percentages relative to generation five; MAF: average minor allele frequency at QTL and neutral loci

ISSN: 1297-9686