Fig. 2

Accuracy of genomic predictions (Holstein only reference) using either 50k SNP data (colored grey) or 50k + a range of ‘top SNPs’ sets (selected from the Holstein QTL discovery set). The ‘top SNPs’ were selected from single-trait GWAS (colored blue) and multi-trait meta-analysis (colored orange) at a less stringent cut-off threshold of − log10(p-value) ≥ 2 [~ 9000 SNPs] and at a more stringent p-value of − log10(p-value) ≥ 3 [~ 2000 SNPs]. Accuracy of predictions are provided for three cow validation sets: a Holsteins, N = 1223), b Jersey, N = 6338), and c Holstein–Jersey crossbreds, N = 790). The traits analysed are heat tolerance milk (HTMYslope), fat (HTFYslope), and protein (HTPYslope) yield slopes. The genomic predictions were generated using either BayesR (50k SNP set) or BayesRC (50k + top SNPs). Vertical lines represent the standard errors calculated from two random validation subsets