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

Table 5 Proportion of variance explained by markers (\(h_{M}^{2}\)) and polygenic effect (\(h_{A}^{2}\)) in the simulated dataset

Data	Analysis	Drop	\(h_{M}^{2}\)	\(h_{A}^{2}\)	\(h^{2}\)
HD	FULL	0.0	0.57	0.02	0.59
S	FULL	0.0	0.63	0.01	0.64
		0.7	0.60	0.02	0.62
		0.9	0.58	0.02	0.60
S	KEPT	0.7	0.59	0.01	0.60
S	KEPT	0.9	0.52	0.05	0.57
S + HD	KEPT + HD	0.7	0.64	0.01	0.65
S + HD	KEPT + HD	0.9	0.62	0.01	0.63

\(h^{2} = h_{M}^{2} + h_{A}^{2}\), HD = HD genotypes used for prediction, S = sequence variants used for prediction, FULL = all variants analysed together, CHR = all variants analysed per chromosome, KEPT = variants selected by CHR reanalysed with all chromosomes together, KEPT + HD = variants selected by CHR and all HD variants reanalysed with all chromosomes together, dropProp = proportion of variants that is dropped after 10,000 MCMC iterations

ISSN: 1297-9686