Fig. 1

Overview of the analyses with the three study scenarios. ‘Scenario 1’: the QTL discovery set was comprised of a subset of 20,623 older Holstein cows (born in 2012 or earlier); the reference set included only Holstein bulls (N = 3323) that were not sires of cows in the discovery set; validation sets included Holsteins, Jersey, and crossbred cows. ‘Scenario 2’: the QTL discovery set was comprised of a combined set of Holsteins (N = 20,623) and Jersey cows (N = 5143); the reference set included only Holstein bulls (N = 3323; as described for “Scenario 1”) that were not sires of the Holstein cows in the discovery set; validation sets included Holstein (N = 1223), Jersey (N = 6338) and crossbred (N = 790) cows. ‘Scenario 3’: the QTL discovery set included only Holstein cows (N = 20,623; as described for “Scenario 1”); the reference set included a combined set of Holsteins (N = 3323) and Jersey (N = 852) bulls); validation sets included Holstein (N = 1223), Jersey (N = 431) and crossbred (N = 790) cows