Predicting daily milk yield for primiparous cows using data of within-herd relatives to capture genotype-by-environment interactions

Abstract

This study develops and illustrates a hybrid k-medoids, random forest, and support vector regression (K-R-S) approach for predicting the lactation curves of individual primiparous cows within a targeted environment using monthly milk production data from their dams and paternal siblings. The model simulation and evaluation were based on historical test-day (TD) milk production data from 2010 to 2016 for 260 Wisconsin dairy farms. Data from older paternal siblings and dams were used to create family units (n = 6,400) of individual calves, from which their future performance was predicted. Test-day milk yield (MY) records from 2010 to 2014 were used for model training, whereas monthly milk production records of Holstein calves born in 2014 were used for model evaluation. The K-R-S hybrid approach was used to generate MY predictions for 5 randomly selected batches of 320 primiparous cows, which were used to evaluate model performance at the individual cow level by cross-validation. Across all 5 batches, the mean absolute error and the root mean square error of the K-R-S predictions were lower (by 24.2 and 23.4%, respectively) than that of the mean daily MY of paternal siblings. The K-R-S predictions of TD MY were closer to actual values 74.2 ± 2.0% of the time, as compared with means of paternal siblings'. The correlation between actual TD MY and K-R-S predictions was greater (0.34 ± 0.01) than the correlation between the actual yield and the mean of paternal siblings (0.08 ± 0.01). The results of this study demonstrate the effectiveness of the K-R-S hybrid approach for predicting future first-lactation MY of dairy calves in management applications, such as milk production forecasting or decision-support simulation, using only monthly TD yields of within-herd relatives and in the absence of detailed genomic data.