Genetic parameters for daily milk weights in U.S. Holsteins using pen-based contemporary groups

Abstract

The availability of daily milk weights and pen location information provides an interesting opportunity to review how contemporary groups are defined for dairy cattle genetic evaluations. In the U.S., dairy cows in larger herds are grouped into pens according to various characteristics like parity, production level, reproductive status, lactation stage, and health status. Our dataset includes pen location information for each daily milk weight, and our goal is to more accurately model contemporary groups when estimating breeding values for daily milk production. Therefore, instead of using herd-year-season, we updated our contemporary group to herd-pen-milking date, thereby capturing the differences in daily milk production more precisely by modeling the true environmental effects cows experience at the pen level. Our dataset includes 21,000,951 aggregated daily milk weights from 114,243 first parity Holstein cows in 157 herds representing 29 U.S. states. Our phenotype is 305-d milk yield or daily milk weight, and both animal and repeatability animal models were used to estimate genetic parameters and breeding values. Age at first calving (6 levels) and days in milk (10 levels) were included as fixed effects and cow (114,243 levels) was included as a random effect. Contemporary group effects included a fixed or random herd-year-season of calving effect (1,492 levels) and/or a fixed or random herd-pen-milking date effect (285,592 levels). Genetic parameters (kg²; posterior SD) were estimated using GIBBSF90+ software, and we found the additive genetic variance for 305-d milk yield was 842,500 (25,093), the herd-year-season variance was 878,960 (33,617), and the residual variance was 1,442,700 (20,438). Whereas for genetic parameters estimated using daily milk weights as the phenotype, the additive genetic variance ranged from 10.48 (0.60) to 24.12 (0.67) the herd-year-season variance was 10.34 (0.40), herd-pen-milking date variance ranged from 4.91 (0.02) to 4.96 (0.02), permanent environmental variance ranged from 10.65 (0.44) to 16.94 (0.30), while the residual variance ranged from 11.81 (0.01) to 14.60 (0.01). Heritability estimates ranged from 0.21 (0.01) to 0.47 (0.01), while repeatability estimates ranged from 0.51 (0.00) to 0.71 (0.00). Although further work is required to disentangle the relationships among contemporary groups, our results suggest value in using daily milk weights and pen-based contemporary groups for genetic evaluation of production traits in dairy cattle.