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

Table 7 Average number of variants per distribution over the number of iterations in the real dataset

Trait	Data	Analysis	DropProp	Number of variants per distribution
Trait	Data	Analysis	DropProp	0 \(\sigma_{g}^{2}\)	0.0001 \(\sigma_{g}^{2}\)	0.001 \(\sigma_{g}^{2}\)	0.01 \(\sigma_{g}^{2}\)
Milk	HD	FULL	0	627,503	4299	22	10
	S	KEPT	0.9	483,521	6603	17	6
	S + HD	KEPT + HD	0.9	1076,643	8927	22	6
Fat	HD	FULL	0	627,510	4312	9	4
	S	KEPT	0.9	483,614	6307	7	4
	S + HD	KEPT + HD	0.9	1080,078	8890	9	3
Prot	HD	FULL	0	627,347	4476	9	3
	S	KEPT	0.9	482,957	6352	8	3
	S + HD	KEPT + HD	0.9	1078,647	9025	9	2
Fert	HD	FULL	0	625,899	5668	260	8
	S	KEPT	0.9	548,382	5715	310	5
	S + HD	KEPT + HD	0.9	1135,712	10,569	436	7

Prot = protein, fert = fertility, 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, dropProp = proportion of variants dropped after 10,000 MCMC iterations, \(\sigma_{g}^{2}\) = additive genetic variance

ISSN: 1297-9686