Integrating genomic and infrared spectral data improves the prediction of milk protein composition in dairy cattle

Genetic evaluations for endangered dual-purpose German Black Pied cattle using 50K SNPs, a breed-specific 200K chip, and whole-genome sequencing

Genetic evaluations of local cattle breeds are hampered due to small reference groups or biased due to the utilization of SNP effects estimated in other large populations. Against this background, there is a lack of studies addressing the possible advantage of whole-genome sequences (WGS) or consideration of specific variants from WGS data in genomic predictions for local breeds with small population size. Consequently, the aim of this study was to compare genetic parameters and accuracies of genomic estimated breeding values (GEBV) for 305-d production traits, fat-to protein ratio (FPR), and somatic cell score (SCS) at the first test date after calving and confirmation traits of the endangered German Black Pied cattle (DSN) breed using 4 different marker panels: (1) the commercial 50K Illumina BovineSNP50 BeadChip, (2) a customized 200K chip designed for DSN (DSN200K) which considers the most important variants for DSN from WGS, (3) randomly generated 200K chips based on WGS data, and (4) a WGS panel. The same number of animals was considered for all marker panel analyses (i.e., 1,811 genotyped or sequenced cows for conformation traits, 2,383 cows for lactation production traits, and 2,420 cows for FPR and SCS). Mixed models for the estimation of genetic parameters directly included the respective genomic relationship matrix from the different marker panels plus the trait-specific fixed effects. For the calculation of GEBV accuracies, we applied repeated random subsampling validation. In the process of separate cross-validations per trait, we created a validation set including 20% of cows with masked phenotypes, and a training set comprising 80% of the cows. The cows were selected randomly in a procedure with 10 replicates considering replacements in the different scenarios. The accuracy was defined as the correlation between the direct GEBV and the phenotypes with subtracted corresponding fixed effects for the cows in the validation set. For FPR and SCS, as well as for lactation production traits, heritabilities were largest based on WGS data, but the increase compared with the 50K or DSN200K applications was quite small in the range from 0.01 to 0.03. Also, for most of the conformation traits, heritabilities were largest based on WGS and DSN200K data, but the increase was in the range of the corresponding standard error. Accordingly, GEBV accuracies for most of the studied traits were highest based on WGS data or when utilizing the DSN200K chip, but the accuracy differences across the marker panels were quite small and nonsignificant. In conclusion, WGS data and the DSN200K chip only contributed to minor improvements in genomic predictions, still justifying the use of the commercial 50K chip. Nevertheless, WGS and the 200KDSN chip harbor breed-specific variants, which are valuable for studying causal genetic mechanisms in the endangered DSN population.

Integrating on-farm and genomic information improves the predictive ability of milk infrared prediction of blood indicators of metabolic disorders in dairy cows

BACKGROUND

Blood metabolic profiles can be used to assess metabolic disorders and to evaluate the health status of dairy cows. Given that these analyses are time-consuming, expensive, and stressful for the cows, there has been increased interest in Fourier transform infrared (FTIR) spectroscopy of milk samples as a rapid, cost-effective alternative for predicting metabolic disturbances. The integration of FTIR data with other layers of information such as genomic and on-farm data (days in milk (DIM) and parity) has been proposed to further enhance the predictive ability of statistical methods. Here, we developed a phenotype prediction approach for a panel of blood metabolites based on a combination of milk FTIR data, on-farm data, and genomic information recorded on 1150 Holstein cows, using BayesB and gradient boosting machine (GBM) models, with tenfold, batch-out and herd-out cross-validation (CV) scenarios.

RESULTS

The predictive ability of these approaches was measured by the coefficient of determination (R²). The results show that, compared to the model that includes only FTIR data, integration of both on-farm (DIM and parity) and genomic information with FTIR data improves the R² for blood metabolites across the three CV scenarios, especially with the herd-out CV: R² values ranged from 5.9 to 17.8% for BayesB, from 8.2 to 16.9% for GBM with the tenfold random CV, from 3.8 to 13.5% for BayesB and from 8.6 to 17.5% for GBM with the batch-out CV, and from 8.4 to 23.0% for BayesB and from 8.1 to 23.8% for GBM with the herd-out CV. Overall, with the model that includes the three sources of data, GBM was more accurate than BayesB with accuracies across the CV scenarios increasing by 7.1% for energy-related metabolites, 10.7% for liver function/hepatic damage, 9.6% for oxidative stress, 6.1% for inflammation/innate immunity, and 11.4% for mineral indicators.

CONCLUSIONS

Our results show that, compared to using only milk FTIR data, a model integrating milk FTIR spectra with on-farm and genomic information improves the prediction of blood metabolic traits in Holstein cattle and that GBM is more accurate in predicting blood metabolites than BayesB, especially for the batch-out CV and herd-out CV scenarios.

Predicting milk protein fractions using infrared spectroscopy and a gradient boosting machine for breeding purposes in Holstein cattle

In recent years, increasing attention has been focused on the genetic evaluation of protein fractions in cow milk with the aim of improving milk quality and technological characteristics. In this context, advances in high-throughput phenotyping by Fourier transform infrared (FTIR) spectroscopy offer the opportunity for large-scale, efficient measurement of novel traits that can be exploited in breeding programs as indicator traits. We took milk samples from 2,558 Holstein cows belonging to 38 herds in northern Italy, operating under different production systems. Fourier transform infrared spectra were collected on the same day as milk sampling and stored for subsequent analysis. Two sets of data (i.e., phenotypes and FTIR spectra) collected in 2 different years (2013 and 2019-2020) were compiled. The following traits were assessed using HPLC: true protein, major casein fractions [α_S1-casein (CN), α_S2-CN, β-CN, κ-CN, and glycosylated-κ-CN], and major whey proteins (β-lactoglobulin and α-lactalbumin), all of which were measured both in grams per liter (g/L) and proportion of total nitrogen (% N). The FTIR predictions were calculated using the gradient boosting machine technique and tested by 3 different cross-validation (CRV) methods. We used the following CRV scenarios: (1) random 10-fold, which randomly split the whole into 10-folds of equal size (9-folds for training and 1-fold for validation); (2) herd/date-out CRV, which assigned 80% of herd/date as the training set with independence of 20% of herd/date assigned as the validation set; (3) forward/backward CRV, which split the data set in training and validation set according with the year of milk sampling (FTIR and gold standard data assessed in 2013 or 2019-2020) using the "old" and "new" databases for training and validation, and vice-versa with independence among them; (4) the CRV for genetic parameters (CRV-gen), where animals without pedigree as assigned as a fixed training population and animals with pedigree information was split in 5-folds, in which 1-fold was assigned to the fixed training population, and 4-folds were assigned to the validation set (independent from the training set). The results (i.e., measures and predictions) of CRV-gen were used to infer the genetic parameters for gold standard laboratory measurements (i.e., proteins assessed with HPLC) and FTIR-based predictions considering the CRV-gen scenario from a bi-trait animal model using single-step genomic BLUP. We found that the prediction accuracies of the gradient boosting machine equations differed according to the way in which the proteins were expressed, achieving higher accuracy when expressed in g/L than when expressed as % N in all CRV scenarios. Concerning the reproducibility of the equations over the different years, the results showed no relevant differences in predictive ability between using "old" data as the training set and "new" data as the validation set and vice-versa. Comparing the additive genetic variance estimates for milk protein fractions between the FTIR predicted and HPLC measures, we found reductions of -19.7% for milk protein fractions expressed in g/L, and -21.19% expressed as % N. Although we found reductions in the heritability estimates, they were small, with values ranging from -1.9 to -7.25% for g/L, and -1.6 to -7.9% for % N. The posterior distributions of the additive genetic correlations (r_a) between the FTIR predictions and the laboratory measurements were generally high (>0.8), even when the milk protein fractions were expressed as % N. Our results show the potential of using FTIR predictions in breeding programs as indicator traits for the selection of animals to enhance milk protein fraction contents. We expect acceptable responses to selection due to the high genetic correlations between HPLC measurements and FTIR predictions.

Association between Days Open and Parity, Calving Season or Milk Spectral Data

Milk spectral data on 2118 cows from nine herds located in northern China were used to access the association of days open (DO). Meanwhile, the parity and calving season of dairy cows were also studied to characterize the difference in DO between groups of these two cow-level factors. The result of the linear mixed-effects model revealed that no significant differences were observed between the parity groups. However, a significant difference in DO exists between calving season groups. The interaction between parity and calving season presented that primiparous cows always exhibit lower DO among all calving season groups, and the variation in DO among parity groups was especially clearer in winter. Survival analysis revealed that the difference in DO between calving season groups might be caused by the different P/AI at the first TAI. In addition, the summer group had a higher chance of conception in the subsequent services than other groups, implying that the micro-environment featured by season played a critical role in P/AI. A weak linkage between DO and wavenumbers ranging in the mid-infrared region was detected. In summary, our study revealed that the calving season of dairy cows can be used to optimize the reproduction management. The potential application of mid-infrared spectroscopy in dairy cows needs to be further developed.

Use of Milk Infrared Spectral Data as Environmental Covariates in Genomic Prediction Models for Production Traits in Canadian Holstein

The purpose of this study was to provide a procedure for the inclusion of milk spectral information into genomic prediction models. Spectral data were considered a set of covariates, in addition to genomic covariates. Milk yield and somatic cell score were used as traits to investigate. A cross-validation was employed, making a distinction for predicting new individuals' performance under known environments, known individuals' performance under new environments, and new individuals' performance under new environments. We found an advantage of including spectral data as environmental covariates when the genomic predictions had to be extrapolated to new environments. This was valid for both observed and, even more, unobserved families (genotypes). Overall, prediction accuracy was larger for milk yield than somatic cell score. Fourier-transformed infrared spectral data can be used as a source of information for the calculation of the 'environmental coordinates' of a given farm in a given time, extrapolating predictions to new environments. This procedure could serve as an example of integration of genomic and phenomic data. This could help using spectral data for traits that present poor predictability at the phenotypic level, such as disease incidence and behavior traits. The strength of the model is the ability to couple genomic with high-throughput phenomic information.