Table 5.

Relationship between haplotype heritability and prediction accuracy for eight traits under the best prediction models

	Trait
	AGW	ADG	BJS	FCR	LMA	LMD	BF	TN
SNP model with additive values (A)
Additive heritability $(\widehat{\text{h}}{}_{\mathrm{\alpha }1}^2)$	0.182	0.186	0.078	0.142	0.327	0.315	0.300	0.297
SNP model with additive and dominance values (A + D)
Additive heritability $(\widehat{\text{h}}{}_{\mathrm{\alpha }2}^2)$	0.173	0.179	0.076	0.139	0.327	0.309	0.299	0.293
Dominance heritability $(\widehat{\text{h}}{}_{\mathrm{\delta }}^2)$	0.045	0.038	0.048	0.036	0.000	0.027	0.028	0.037
SNP broad-sense heritability $(\widehat{\text{h}}{}_{\text{s}}^2)$	0.218	0.216	0.124	0.175	0.327	0.336	0.326	0.331
Haplotype prediction models
Best model	H	H	H	D + H	H	A + D + H	A + D + H	A + D + H
Best haplotype blocking method	500 Kb	500 Kb	100 Kb	1 Mb	Genes	Genes	1 Mb	Genes
Accuracy increase (%)	7.14	6.56	7.36	4.95	2.74	1.92	1.29	0.25
SNP additive heritability $(\widehat{\text{h}}{}_{\mathrm{\alpha }\text{s}}^2)$	–	–	–	–	–	0.101	0.154	0.137
SNP dominance heritability $(\widehat{\text{h}}{}_{\mathrm{\delta }\text{s}}^2)$	–	–	–	0.036	–	0.026	0.022	0.037
Haplotype additive heritability $(\widehat{\text{h}}{}_{\mathrm{\alpha }\text{h}}^2)$	0.208	0.213	0.097	0.170	0.336	0.215	0.183	0.162
Total heritability $(\widehat{\text{h}}{}_{\text{g}}^2)$	0.208	0.213	0.097	0.206	0.336	0.343	0.359	0.336
Estimates of haplotype epistasis heritability
Haplotype epistasis heritability $(\widehat{\text{h}}{}_{\text{g}}^2)$	0.026	0.027	0.019	0.031	0.009	0.007	0.033	0.005
Relative haplotype epistasis heritability $(\widehat{\text{h}}{}_{\text{Er}}^2,\%)$	14.29	14.52	24.36	22.30	2.75	2.26	11.04	1.71

Accuracy increase is the percentage increase in observed prediction accuracy of the best haplotype model relative to the accuracy of the best SNP model (in italic font) using the original phenotypic values

A SNP additive values, D SNP dominance values, H haplotype additive values, AGW age at 100 kg live weight, ADG daily gain, BJS body judging score, FCR feed conversion ratio, LMA loin muscle area, LMD loin muscle depth, BF back fat thickness, TN teat number