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Table 8 Proportion of variance explained by prediction markers (\(h_{M}^{2}\)) and polygenic effect (\(h_{A}^{2}\))

From: Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect

Trait Data Analysis DropProp \(h_{M}^{2}\) \(h_{A}^{2}\) \(h^{2}\)
Milk HD FULL 0.0 0.29 0.16 0.45
S KEPT 0.9 0.49 0.05 0.53
S + HD KEPT + HD 0.9 0.53 0.04 0.57
Fat HD FULL 0.0 0.22 0.15 0.37
S KEPT 0.9 0.39 0.04 0.42
S + HD KEPT + HD 0.9 0.44 0.03 0.47
Protein HD FULL 0.0 0.21 0.16 0.37
S KEPT 0.9 0.39 0.05 0.43
S + HD KEPT + HD 0.9 0.44 0.04 0.48
Fertility HD FULL 0.0 0.02 0.00 0.02
S KEPT 0.9 0.03 0.00 0.03
S + HD KEPT + HD 0.9 0.04 0.00 0.04
  1. \(h^{2} = h_{M}^{2} + h_{A}^{2}\), HD = high density SNP, HD = HD genotypes used for prediction, S = sequence variants used for prediction, FULL = all variants analysed together, KEPT = variants selected per chromosome reanalysed with all chromosomes together, KEPT + HD = variants selected per chromosome and all HD variants reanalysed with all chromosomes together, drop = proportion of variants dropped after 10,000 MCMC iterations
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