For example, in the CI of QTL ID 42 (BTA5), detected for UD in HOL, we found a variant at 88,862,824 bp that also had, for the same trait, a significant effect in MON cows (− log 10 (P) = 7.4, results not shown) and an effect close to significance in MON bulls (− log 10 (P) = 7.2).
First, it is important to note that nearly all the highly significant QTL and all the QTL present in several breeds or affecting several traits were confirmed.
Within a QTL region, the effects of variants with the highest imputation accuracy, which are not necessarily the same across breeds, were probably estimated more accurately and were thus more likely to be significant.