Comparison of Bayesian regression models and partial least squares regression for the development of infrared prediction equations

The aim of this study was to compare the common method of exploiting infrared spectral data in animal breeding; that is, estimating the breeding values for the traits predicted by infrared spectroscopy, and an alternative approach based on the direct use of spectral information (direct prediction, DP) to predict the estimated breeding values (EBV). Traits were pH, milk coagulation properties, contents of the main casein and whey protein fractions, cheese yield measured by micro-cheese making, lactoferrin, Ca, and fat composition. For the DP method, the number of spectral variables was reduced by principal components analysis to 8 latent traits that explained 99% of the original spectral variation. Restricted maximum likelihood was used to estimate variance components of the latent traits. (Co)variance components of the original spectral traits were obtained by back-transformation and EBV of all derived milk traits were then predicted as traits correlated with the genetic information of the spectra. The rank correlation between the EBV obtained for the infrared-predicted traits and those obtained from the DP method was variable across traits. Rank correlations ranged from 0.07 (for the content of saturated fatty acids expressed as g/100 g of fat) to 0.96 (for dry matter cheese yield, %) and, for most traits, was <0.5. This result can be explained by the nature of the principal components analysis: it does not take into account the covariance between the spectral variables and the reference traits but produces latent traits that maximize the spectral variance explained. Thus, the direct approach is more likely to be effective for traits more related to the main sources of spectral variation (i.e., protein and fat). More research is required to study spectral genetic variation and to determine the best way to choose spectral regions and the type and number of considered latent traits for potential applications.