Abstract
BackgroundOver the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. Genomic data might help predict these phenotypes when integrated with milk FTIR spectra. The objective of this study was to investigate prediction accuracy for milk protein phenotypes when heterogeneous on-farm, genomic, and pedigree data were integrated with the spectra. To this end, we used the records of 966 Italian Brown Swiss cows with milk FTIR spectra, on-farm information, medium-density genetic markers, and pedigree data. True and total whey protein, and five casein, and two whey protein traits were analyzed. Multiple kernel learning constructed from spectral and genomic (pedigree) relationship matrices and multilayer BayesB assigning separate priors for FTIR and markers were benchmarked against a baseline partial least squares (PLS) regression. Seven combinations of covariates were considered, and their predictive abilities were evaluated by repeated random sub-sampling and herd cross-validations (CV).ResultsAddition of the on-farm effects such as herd, days in milk, and parity to spectral data improved predictions as compared to those obtained using the spectra alone. Integrating genomics and/or the top three markers with a large effect further enhanced the predictions. Pedigree data also improved prediction, but to a lesser extent than genomic data. Multiple kernel learning and multilayer BayesB increased predictive performance, whereas PLS did not. Overall, multilayer BayesB provided better predictions than multiple kernel learning, and lower prediction performance was observed in herd CV compared to repeated random sub-sampling CV.ConclusionsIntegration of genomic information with milk FTIR spectral can enhance milk protein trait predictions by 25% and 7% on average for repeated random sub-sampling and herd CV, respectively. Multiple kernel learning and multilayer BayesB outperformed PLS when used to integrate heterogeneous data for phenotypic predictions.
Highlights
Over the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes
When on-farm predictors were added to the models, R2 increased, except for β-CN, ranging from 0.20 to 0.92
The small difference observed in R2 between Model 2 (M2) and Model 3 (M3) indicates that days in milk (DIM) and parity made only small contributions compared to the herd effect
Summary
Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. The objective of this study was to investigate prediction accuracy for milk protein phenotypes when heterogeneous on-farm, genomic, and pedigree data were integrated with the spectra. To this end, we used the records of 966 Italian Brown Swiss cows with milk FTIR spectra, on-farm information, medium-density genetic markers, and pedigree data. Baba et al Genet Sel Evol (2021) 53:29 develop equations for predicting complex traits that are difficult and expensive to measure because of high phenotyping costs These include milk fatty acids [5], energy intake [6], methane emissions [7], and metabolic profiles [8]. Milk FTIR spectra can be used for genetic improvement when there are strong additive genetic correlations between target traits and FTIR predictions [17, 18]
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