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

Table 4 Mean phenotype, observed homozygosity (\({H}_{o}\)) at the non-SNP loci and the QTL in the commercial population when using the MCM or MS strategy based on the true additive and dominance effect and the genotypes of the QTL under different gene actions

	DOM_VAR		DOM_EQU_10		DOM_EQU_100		DIR_VAR		DOM_EQU_1000
	MCM	MS	MCM	MS	MCM	MS	MCM	MS	MCM	MS
t = 1
Phenotype	1.14	1.50	0.94	0.74	1.10	1.31	1.13	1.48	1.29	1.5
Ho non-SNP	0.52	0.53	0.52	0.53	0.52	0.52	0.52	0.52	0.52	0.52
Ho QTL	0.52	0.53	0.58	0.35	0.53	0.47	0.52	0.51	0.52	0.51
t = 4
Phenotype	3.68	4.00	1.49	1.40	2.88	3.09	3.16	3.54	3.20	3.61
Ho non-SNP	0.54	0.55	0.54	0.55	0.54	0.54	0.54	0.53	0.54	0.53
Ho QTL	0.55	0.55	0.99	0.78	0.58	0.52	0.54	0.52	0.53	0.51

Standard errors range from 0.02 to 0.03 for mean phenotype and are always lower than 0.01 for observed homozygosity
MCM minimum coancestry mating, MS mate selection, 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