Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle

Table 5 Differences in reliability between the WB-50 K model and other models (Δ_max) for within-breed prediction

Breed	Trait	WB-50 K + WBQTLt	WB-50 K + MBQTLt	WB-50 K + MBQTLt-n/w
HOLDK	Milk yield	0.02	0.03	0.05
	Fat yield	0.04	0.05	0.05
	Protein yield	−0.01	0.01	0.03
HOLFR	Milk yield	0.02	0.03	0.04
	Fat yield	0.05	0.05	0.05
	Protein yield	0.02	0.03	0.03
JER	Milk yield	0.04	0.07	0.10
	Fat yield	0.02	0.01	0.02
	Protein yield	0.00	0.02	0.05
RDC	Milk yield	0.00	0.05	0.06
	Fat yield	−0.01	0.03	0.07
	Protein yield	−0.01	0.01	0.05

The table provides only the Δ_max, i.e. the difference (Δ) obtained with the QTL set that resulted in the highest reliability
The QTL component consisted of all the variants selected with a p value less than a threshold for the within-breed GWAS (WB-50 K + WBQTLt) and the multi-breed GWAS (WB-50 K + MBQTLt), or of a limited number of SNPs per QTL interval that were selected with p value less than a threshold for the multi-breed GWAS (WB-50 K + MBQTLt-n/w)
HOLDK Danish Holstein, HOLFR French Holstein, JER Jersey, RDC Danish Red

ISSN: 1297-9686