Comparison of Single-Breed and Multi-Breed Training Populations for Infrared Predictions of Novel Phenotypes in Holstein Cows

In general, Fourier-transform infrared (FTIR) predictions are developed using a single-breed population split into a training and a validation set. However, using populations formed of different breeds is an attractive way to design cross-validation scenarios aimed at increasing prediction for difficult-to-measure traits in the dairy industry. This study aimed to evaluate the potential of FTIR prediction using training set combining specialized and dual-purpose dairy breeds to predict different phenotypes divergent in terms of biological meaning, variability, and heritability, such as body condition score (BCS), serum β-hydroxybutyrate (BHB), and kappa casein (k-CN) in the major cattle breed, i.e., Holstein-Friesian. Data were obtained from specialized dairy breeds: Holstein (468 cows) and Brown Swiss (657 cows), and dual-purpose breeds: Simmental (157 cows), Alpine Grey (75 cows), and Rendena (104 cows), giving a total of 1461 cows from 41 multi-breed dairy herds. The FTIR prediction model was developed using a gradient boosting machine (GBM), and predictive ability for the target phenotype in Holstein cows was assessed using different cross-validation (CV) strategies: a within-breed scenario using 10-fold cross-validation, for which the Holstein population was randomly split into 10 folds, one for validation and the remaining nine for training (10-fold_HO); an across-breed scenario (BS_HO) where the Brown Swiss cows were used as the training set and the Holstein cows as the validation set; a specialized multi-breed scenario (BS+HO_10-fold), where the entire Brown Swiss and Holstein populations were combined then split into 10 folds, and a multi-breed scenario (Multi-breed), where the training set comprised specialized (Holstein and Brown Swiss) and dual-purpose (Simmental, Alpine Grey, and Rendena) dairy cows, combined with nine folds of the Holstein cows. Lastly a Multi-breed CV2 scenario was implemented, assuming the same number of records as the reference scenario and using the same proportions as the multi-breed. Within-Holstein, FTIR predictions had a predictive ability of 0.63 for BCS, 0.81 for BHB, and 0.80 for k-CN. Using a specific breed (Brown Swiss) as the training set for prediction in the Holstein population reduced the prediction accuracy by 10% for BCS, 7% for BHB, and 11% for k-CN. Notably, the combination of Holstein and Brown Swiss cows in the training set increased the predictive ability of the model by 6%, which was 0.66 for BCS, 0.85 for BHB, and 0.87 for k-CN. Using multiple specialized and dual-purpose animals in the training set outperforms the 10-fold_HO (standard) approach, with an increase in predictive ability of 8% for BCS, 7% for BHB, and 10% for k-CN. When the Multi-breed CV2 was implemented, no improvement was observed. Our findings suggest that FTIR prediction of different phenotypes in the Holstein breed can be improved by including different specialized and dual-purpose breeds in the training population. Our study also shows that predictive ability is enhanced when the size of the training population and the phenotypic variability are increased.