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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