Haplotype genomic prediction of phenotypic values based on chromosome distance and gene boundaries using low-coverage sequencing in Duroc pigs

Table 4 Observed accuracy of predicting original and corrected phenotypic values for the best SNP and haplotype models

	Trait
	AGW	ADG	BJS	FCR	LMA	LMD	BF	TN	Mean
Best SNP prediction model (as defined in Table 3)
\({ \hat{\text{R}}}{^{\text{s}}_{0\text{y}}}\)	0.252	0.259	0.258	0.202	0.402	0.364	0.387	0.405	0.316
\({\hat{\text{R}}}{^{\text{s}}_{0\text{r}}}\)	0.256	0.262	0.138	0.204	0.415	0.394	0.399	0.407	0.309
Haplotype prediction accuracy
Best model	H	H	H	D + H	H	A + D + H	A + D + H	A + D + H
Best blocking	500 kb	500 kb	100 kb	1 Mb	Genes	Genes	1 Mb	Genes
\({ \hat{\text{R}}}{_{0\text{y}}^{\text{h}}}\)	0.270	0.276	0.277	0.212	0.413	0.371	0.392	0.406	0.327
\({\hat{\text{R}}}{_{0\text{r}}^{\text{h}}}\)	0.269	0.274	0.157	0.211	0.426	0.400	0.403	0.409	0.319
\({\hat{\text{R}}}{^{\text{s}}_{0\text{y}}}/{\hat{\text{R}}}{^{\text{s}}_{0\text{r}}}-1,\%\)	− 1.0	0.5	88.9	− 1.5	0.3	− 2.9	− 1.7	− 3.6
\({\hat{\text{R}}}{^{\text{h}}_{0\text{y}}}/{\hat{\text{R}}}{^{\text{h}}_{0\text{r}}}-1,\%\)	0.7	2.7	74.6	0.3	− 0.2	− 2.4	− 1.8	− 3.8

\({\hat{\text{R}}}{^{\text{s}}_{0\text{y}}}\), observed accuracy of predicting phenotypic values by the best SNP model using the original phenotypic values; \({\hat{\text{R}}}{^{\text{s}}_{0\text{r}}}\), observed accuracy of predicting phenotypic values by the best SNP model using the corrected phenotypic values; \({\hat{\text{R}}}{^{\text{h}}_{0\text{y}}}\), observed accuracy of predicting phenotypic values by the best haplotype model using the original phenotypic values; \({\hat{\text{R}}}{^{\text{h}}_{0\text{r}}}\), observed accuracy of predicting phenotypic values by the best haplotype model using the corrected 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

ISSN: 1297-9686