Effect of genomic selection and genotyping strategy on estimation of variance components in animal models using different relationship matrices

Table 5 Average VC estimates across replicates (averaged standard error) in the simulation study

Selection method in simulation	Analysis model	Analysis genotyping strategy and proportion (%)		\(\hat{\sigma }_{a}^{2}\) (SE)	\(\hat{\sigma }_{e}^{2}\) (SE)
Scenario 1: H-AM with 20% selective genotyping in SR21-40	H-AM	Selective	10	13,358 (635)^ab	22,358 (324)^ab
			20	40,597 (729)^ab	11,904 (243)^ab
			30	55,051 (639)^ab	8695 (136)^ab
		Random	10	9265 (469)	24,231 (270)^ab
			20	8967 (440)	24,382 (243)
			30	8873 (421)	24,461 (223)
	A-AM			11,475 (544)^ab	23,148 (312)⁵⁶
Scenario 2: H-AM with 20% random genotyping in SR21-40	H-AM	Selective	10	13,370 (641)^ab	22,379 (328)^ab
			20	43,302 (697)^ab	10,911 (223)^ab
			30	55,735 (635)^ab	8462 (133)^ab
		Random	10	8645 (449)^b	24,581 (265)
			20	8408 (423)^b	24,729 (241)
			30	8507 (410)^b	24,689 (222)
	A-AM			9598 (477)^a	24,125 (289)^ab
Scenario 3: A-AM in SR1-40	H-AM	Selective	10	11,402 (561)^ab	23,346 (305)^ab
			20	37,343 (735)^ab	12,947 (260)^ab
			30	53,307 (633)^ab	9037 (142)^ab
		Random	10	8347 (441)^b	24,825 (267)
			20	8427 (425)^b	24,789 (244)
			30	8470 (404)^b	24,740 (223)
	A-AM			8206 (433)^b	24,902 (278)

\(\hat{\sigma }_{a}^{2}\): genetic variance; \(\hat{\sigma }_{e}^{2}\): residual variance
H-AM animal model with combined pedigree-based and genomic relationship matrix, A-AM animal model with pedigree-based relationship matrix
^aSignificantly different from the A-AM variance in Scenario 3 (P < 0.05)
^bSignificantly different from the base-population variances (P < 0.05)

ISSN: 1297-9686