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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