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Table 5 Relationship between haplotype heritability and prediction accuracy for eight traits under the best prediction 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
SNP model with additive values (A)
 Additive heritability \({(\hat{\text{h}}}{_{{\upalpha }1}^{2}})\) 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 \({(\hat{\text{h}}}{_{{\upalpha }2}^{2}})\) 0.173 0.179 0.076 0.139 0.327 0.309 0.299 0.293
 Dominance heritability \({(\hat{\text{h}}}{_{\updelta }^{2}})\) 0.045 0.038 0.048 0.036 0.000 0.027 0.028 0.037
 SNP broad-sense heritability \({(\hat{\text{h}}}{_{\text{s}}^{2}})\) 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 \({(\hat{\text{h}}}{_{{\upalpha} {\text{s}}}^{2}})\) 0.101 0.154 0.137
 SNP dominance heritability \({(\hat{\text{h}}}{_{{\updelta} {\text{s}}}^{2}})\) 0.036 0.026 0.022 0.037
 Haplotype additive heritability \({(\hat{\text{h}}}{_{{\upalpha} {\text{h}}}^{2}})\) 0.208 0.213 0.097 0.170 0.336 0.215 0.183 0.162
 Total heritability \({(\hat{\text{h}}}{_{\text{g}}^{2}})\) 0.208 0.213 0.097 0.206 0.336 0.343 0.359 0.336
Estimates of haplotype epistasis heritability
 Haplotype epistasis heritability \({(\hat{\text{h}}}{_{\text{g}}^{2}})\) 0.026 0.027 0.019 0.031 0.009 0.007 0.033 0.005
 Relative haplotype epistasis heritability \({(\hat{\text{h}}}{_{\text{Er}}^{2}}, \%)\) 14.29 14.52 24.36 22.30 2.75 2.26 11.04 1.71
  1. 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
  2. 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