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

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

  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  
  1. \({\hat{\text{R}}}{^{\text{s}}_{0\text{y}}}\), 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