Table 2.

P-value thresholds, number of SNPs with significant dominance effects and corresponding false discovery rates (FDR) for milk yield (MY) and calving interval (CI) in discovery and validation populations

	Discovery			Individual validation				Segment validation
Trait	P-value threshold	Holstein discovery (7055)	FDR (%)	P-value threshold	Jersey validation (3795)	FDR (%)	No. Same Dir.a	P-value threshold	Jersey validation (3795)	FDR (%)
MY	0.0001	40	102	0.01	1	39	0	0.01	21	1
CI	0.0001	36	113	0.01	3	11	1	0.01	10	3

^aNumber of same direction SNP effects in discovery and validation populations