Effects of breed, farm intensiveness, and cow productivity level on cheese-making ability predicted using infrared spectral data at the population level

Fourier-transform infrared (FTIR) spectra collected during milk recording schemes at population level can be used for predicting novel traits of interest for farm management, cows' genetic improvement, and milk payment systems. The aims of this study were as follows. (1) To predict cheese yield traits using FTIR spectra from routine milk recordings exploiting previously developed calibration equations. (2) To compare the predicted cheese-making abilities of different dairy and dual-purpose breeds. (3) To analyze the effects of herds' level of intensiveness (HL) and of the cow's level of productivity (CL). (4) To compare the patterns of predicted cheese yields with the patterns of milk composition in different breeds to discern the drivers of cheese-making efficiency. The major sources of variation of FTIR predictions of cheese yield ability (fresh cheese or cheese solids produced per unit milk) of individual milk samples were studied on 115,819 cows of 4 breeds (2 specialized dairy breeds, Holstein and Brown Swiss, and 2 dual-purpose breeds, Simmental and Alpine Grey) from 6,430 herds and exploiting 1,759,706 FTIR test-day spectra collected over 7 yr of milk sampling. Calibration equations used were previously developed on 1,264 individual laboratory model cheese procedures (cross-validation R² 0.85 and 0.95 for fresh and solids cheese yields, respectively). The linear model used for statistical analysis included the effects of parity, lactation stage, year of calving, month of sampling, HL, CL, breed of cow, and the interactions breed × HL and breed × CL. The HL and CL stratifications (5 classes each) were based on average daily secretion of milk net energy per cow. All effects were highly significant (P < 0.001). The major conclusions were as follows. (1) The FTIR-based prediction of cheese yield of milk goes beyond the knowledge of fat and protein content, partially explaining differences in cheese-making ability in different cows, breeds and herds. (2) Differences in cheese yields of different breeds are only partially explained by milk fat and protein composition, and less productive breeds are characterized by a higher milk nutrient content as well as a higher recovery of nutrients in the cheese. (3) High-intensive herds not only produce much more milk, but the milk has a higher nutrient content and a higher cheese yield, whereas within herds, compared with less productive cows, the more productive cows have a much greater milk yield, milk with a greater content of fat but not of protein, and a moderate improvement in cheese yield, differing little from expectations based on milk composition. Finally, (4) the effects of HL and CL on milk quality and cheese-making ability are similar but not identical in different breeds, the less productive ones having some advantage in terms of cheese-making ability. We can obtain FTIR-based prediction of cheese yield from individual milk samples retrospectively at population level, which seems to go beyond the simple knowledge of milk composition, incorporating information on nutrient retention ability in cheese, with possible advantages for management of farms, genetic improvement of dairy cows, and milk payment systems.