Table 1.

P-value thresholds, number of SNPs found to be additively significant 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	10−7	715	0	10−5	93	0	64	10−5	413	0
CI	0.0001	136	30	0.01	5	26	5	0.01	73	1

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