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

Table 1 Mean phenotype in the commercial population at generations (\(t\)) 1 and 4 when using MCM or MS based on the genotypes of a variable number of SNPs (n_SNP) 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	MCM	MS	MCM	MS	MCM	MS	MCM	MS	MCM	MS	MCM	MS
t = 1
100	0.60	0.60	0.57	0.60	0.50	0.51	0.55	0.50	0.82	0.52	0.61	0.39
1000	0.78	0.77	0.74	0.80	0.60	0.55	0.71	0.45	0.83	0.23	0.86	0.12
10,000	0.81	0.81	0.79	0.88	0.62	0.48	0.76	0.08	0.92	− 0.73	0.94	− 1.03
100,000	0.81	0.81	0.80	0.90	0.65	0.46	0.78	− 0.05	0.93	− 1.17	0.97	− 1.65
200,000	0.87	0.87	0.84	0.96	0.69	0.53	0.84	− 0.01	0.98	− 1.17	1.02	− 1.63
t = 4
100	1.64	1.64	1.69	1.71	1.06	1.04	1.28	1.17	1.47	1.15	0.98	0.66
1000	2.58	2.57	2.59	2.63	1.31	1.29	2.01	1.90	2.09	1.79	1.96	1.55
10,000	2.80	2.80	2.85	2.92	1.36	1.34	2.23	2.07	2.39	1.92	2.27	1.75
100,000	2.81	2.80	2.88	2.96	1.36	1.35	2.24	2.05	2.42	1.88	2.33	1.68
200,000	2.86	2.85	2.94	3.03	1.38	1.36	2.30	2.10	2.44	1.89	2.39	1.75

Standard errors ranged from 0.02 to 0.13
MCM minimum coancestry mating, MS mate selection, 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