The genetic architecture of milk urea concentration in dairy cattle differs across the lactation cycle.

Milk urea concentration (MUC) is an indicator of dietary protein utilization and nitrogen use efficiency in dairy cows. We performed GWAS on MUC in early, mid, and late lactation in the Holstein (HOL) and Brown Swiss (BSW) dairy cattle breeds using imputed sequence variants. We identified 11 and 17 independent QTL for MUC across the 3 lactation stages in BSW and HOL, respectively. Although many of these QTL have previously been reported for MUC and other dairy traits, our study provides evidence that some QTL exert lactation stage-specific effects. Our findings suggest that variants at the DGAT1 locus on BTA14 have pleiotropic effects on MUC and other dairy traits. This QTL showed an early lactation-specific association with MUC but affected milk and fat yield across the entire lactation. We fine-mapped 2 QTL for MUC in early and mid lactation in BSW on BTA9 (lead SNP: 9:21392941, β = 0.6510) and BTA28 (lead SNP: 28:6518357; β = -0.5020). We identified long noncoding RNA ENSBTAG00000058688 and IBTK as positional and functional candidate genes for the BTA9 QTL, and KCNK1 as positional and functional candidate gene that harbors a highly significant missense variant for the BTA28 QTL. In conclusion, our results shed light on the genetic architecture of MUC and highlighted QTL harboring potential functional variants underpinning milk urea variation within and across breeds.