Optimum mating designs for exploiting dominance in genomic selection schemes for aquaculture species

Table 2 Accuracy of estimates of breeding values (Add) and dominance deviations (Dom) based on the genotypes of a variable number of SNPs (n_SNP) at generations (\(t\)) 1 and 4 for different types of gene action

n_SNP	ADD_VAR		DOM_VAR		DOM_EQU_10		DOM_EQU_100		DIR_VAR		DOM_EQU_1000
n_SNP	Add	Dom	Add	Dom	Add	Dom	Add	Dom	Add	Dom	Add	Dom
t = 1
100	0.53	–	0.47	0.16	0.47	0.16	0.46	0.16	0.57	0.28	0.42	0.23
1000	0.73	–	0.68	0.32	0.68	0.32	0.67	0.32	0.62	0.37	0.59	0.39
10,000	0.76	–	0.73	0.42	0.72	0.42	0.71	0.43	0.66	0.47	0.63	0.50
100,000	0.77	–	0.73	0.43	0.73	0.43	0.72	0.45	0.66	0.49	0.63	0.51
200,000	0.77	–	0.73	0.43	0.73	0.45	0.72	0.44	0.66	0.49	0.66	0.51
t = 4
100	0.32	–	0.32	0.09	0.26	0.08	0.30	0.09	0.39	0.13	0.30	0.10
1000	0.65	–	0.63	0.27	0.39	0.21	0.57	0.27	0.58	0.30	0.57	0.29
100,00	0.74	–	0.73	0.46	0.45	0.36	0.66	0.46	0.67	0.47	0.66	0.47
100,000	0.75	–	0.74	0.50	0.47	0.40	0.67	0.50	0.69	0.52	0.68	0.51
200,000	0.75	–	0.74	0.51	0.46	0.40	0.68	0.51	0.69	0.51	0.69	0.53

Standard errors were lower than 0.02
ADD_VAR only additive effects normally distributed, DOM_VAR additive and dominance effects normally distributed, DIR_VAR as in DOM_VAR but with dominance effects all positive, DOM_EQU_x all effects equal with d = a being × the number of QTL (actually 10, 100 or 1000)

ISSN: 1297-9686