Table 5.

Minor allele frequencies for each top QTL variant

Phenotype	Variant	MAF All	HF (N = 8930)	J (N = 3599)	Cross (N = 15,652)
FY (kg/day)	rs466308089	0.031	0.042	0.002	0.032
PY (kg/day)	rs108985709	0.409	0.483	0.298	0.391
MY (L/day)	rs208473130	0.444	0.489	0.390	0.435
FC (%)	rs379739117	0.473	*0.476	0.391	0.464
PC (%)	rs208375076	0.446	0.492	0.391	0.437
MY (%)	rs378861677	0.116	0.182	0.010	0.101
PC (%)	rs210293314	0.276	0.333	0.184	0.264

Allele frequencies are shown across the entire study population of cows and by breed (HF Holstein–Friesian; J Jersey)

Asterisks (*) indicate breeds where the minor allele differs from that for the population as a whole. The markers listed in the top section of the table tag the primary QTL for each phenotype, while those listed in the bottom section tag secondary QTL