The evolving role of Fourier-transform mid-infrared spectroscopy in genetic improvement of dairy cattle

Over the last 100 years, significant advances have been made in the characterisation of milk composition for dairy cattle improvement programs. Technological progress has enabled a shift from labour intensive, on-farm collection and processing of samples that assess yield and fat levels in milk, to large-scale processing of samples through centralised laboratories, with the scope extended to include quantification of other traits. Fourier-transform mid-infrared (FT-MIR) spectroscopy has had a significant role in the transformation of milk composition phenotyping, with spectral-based predictions of major milk components already being widely used in milk payment and animal evaluation systems globally. Increasingly, there is interest in analysing the individual FT-MIR wavenumbers, and in utilising the FT-MIR data to predict other novel traits of importance to breeding programs. This includes traits related to the nutritional value of milk, the processability of milk into products such as cheese, and traits relevant to animal health and the environment. The ability to successfully incorporate these traits into breeding programs is dependent on the heritability of the FT-MIR predicted traits, and the genetic correlations between the FT-MIR predicted and actual trait values. Linking FT-MIR predicted traits to the underlying mutations responsible for their variation can be difficult because the phenotypic expression of these traits are a function of a diverse range of molecular and biological mechanisms that can obscure their genetic basis. The individual FT-MIR wavenumbers give insights into the chemical composition of milk and provide an additional layer of granularity that may assist with establishing causal links between the genome and observed phenotypes. Additionally, there are other molecular phenotypes such as those related to the metabolome, chromatin accessibility, and RNA editing that could improve our understanding of the underlying biological systems controlling traits of interest. Here we review topics of importance to phenotyping and genetic applications of FT-MIR spectra datasets, and discuss opportunities for consolidating FT-MIR datasets with other genomic and molecular data sources to improve future dairy cattle breeding programs.

Potential of milk mid-infrared spectra to predict nitrogen use efficiency of individual dairy cows in early lactation

Improving nitrogen use efficiency (NUE) at both the individual cow and the herd level has become a key target in dairy production systems, for both environmental and economic reasons. Cost-effective and large-scale phenotyping methods are required to improve NUE through genetic selection and by feeding and management strategies. The aim of this study was to evaluate the possibility of using mid-infrared (MIR) spectra of milk to predict individual dairy cow NUE during early lactation. Data were collected from 129 Holstein cows, from calving until 50 d in milk, in 3 research herds (Denmark, Ireland, and the UK). In 2 of the herds, diets were designed to challenge cows metabolically, whereas a diet reflecting local management practices was offered in the third herd. Nitrogen intake (kg/d) and nitrogen excreted in milk (kg/d) were calculated daily. Nitrogen use efficiency was calculated as the ratio between nitrogen in milk and nitrogen intake, and expressed as a percentage. Individual daily values for NUE ranged from 9.7 to 81.7%, with an average of 36.9% and standard deviation of 10.4%. Milk MIR spectra were recorded twice weekly and were standardized into a common format to avoid bias between apparatus or sampling periods. Regression models predicting NUE using milk MIR spectra were developed on 1,034 observations using partial least squares or support vector machines regression methods. The models were then evaluated through (1) a cross-validation using 10 subsets, (2) a cow validation excluding 25% of the cows to be used as a validation set, and (3) a diet validation excluding each of the diets one by one to be used as validation sets. The best statistical performances were obtained when using the support vector machines method. Inclusion of milk yield and lactation number as predictors, in combination with the spectra, also improved the calibration. In cross-validation, the best model predicted NUE with a coefficient of determination of cross-validation of 0.74 and a relative error of 14%, which is suitable to discriminate between low- and high-NUE cows. When performing the cow validation, the relative error remained at 14%, and during the diet validation the relative error ranged from 12 to 34%. In the diet validation, the models showed a lack of robustness, demonstrating difficulties in predicting NUE for diets and for samples that were not represented in the calibration data set. Hence, a need exists to integrate more data in the models to cover a maximum of variability regarding breeds, diets, lactation stages, management practices, seasons, MIR instruments, and geographic regions. Although the model needs to be validated and improved for use in routine conditions, these preliminary results showed that it was possible to obtain information on NUE through milk MIR spectra. This could potentially allow large-scale predictions to aid both further genetic and genomic studies, and the development of farm management tools.

Short communication: Investigation of the temporal relationships between milk mid-infrared predicted biomarkers and lameness events in later lactation

This study reports on the exploration of temporal relationships between milk mid-infrared predicted biomarkers and lameness events. Lameness in dairy cows is an issue that can vary greatly in severity and is of concern for both producers and consumers. Metabolic disorders are often associated with lameness. However, lameness can arise weeks or even months after the metabolic disorder, making the detection of causality difficult. We already use mid-infrared technology to predict major milk components, such as fat or protein, during routine milk recording and for milk payment. It was recently shown that this technology can also be used to predict novel biomarkers linked to metabolic disorders in cows, such as oleic acid (18:1 cis-9), β-hydroxybutyrate, acetone, and citrate in milk. We used these novel biomarkers as proxies for metabolic issues. Other studies have explored the possibility of using mid-infrared spectra to predict metabolic diseases and found it (potentially) usable for indicating classes of metabolic problems. We wanted to explore the possible relationship between mid-infrared-based metabolites and lameness over the course of lactation. In total, data were recorded from 6,292 cows on 161 farms in Austria. Lameness data were recorded between March 2014 and March 2015 and consisted of 37,555 records. Mid-infrared data were recorded between July and December 2014 and consisted of 9,152 records. Our approach consisted of fitting preadjustments to the data using fixed effects, computing pair-wise correlations, and finally applying polynomial smoothing of the correlations for a given biomarker at a certain month in lactation and the lameness events scored on severity scale from sound or non-lame (lameness score of 1) to severely lame (lameness score of 5) throughout the lactation. The final correlations between biomarkers and lameness scores were significant, but not high. However, for the results of the present study, we should not look at the correlations in terms of absolute values, but rather as indicators of a relationship through time. When doing so, we can see that metabolic problems occurring in mo 1 and 3 seem more linked to long-term effects on hoof and leg health than those in mo 2. However, the quantity (only 1 pair-wise correlation exceeded 1,000 observations) and the quality (due to limited data, no separation according to more metabolic-related diseases could be done) of the data should be improved.

Genetic analysis of orotic acid predicted with Fourier transform infrared milk spectra

Fourier transform infrared spectral analysis is a cheap and fast method to predict milk composition. A not very well studied milk component is orotic acid. Orotic acid is an intermediate in the biosynthesis pathway of pyrimidine nucleotides and is an indicator for the metabolic cattle disorder deficiency of uridine monophosphate synthase. The function of orotic acid in milk and its effect on calf health, health of humans consuming milk or milk products, manufacturing properties of milk, and its potential as an indicator trait are largely unknown. The aims of this study were to determine if milk orotic acid can be predicted from infrared milk spectra and to perform a large-scale phenotypic and genetic analysis of infrared-predicted milk orotic acid. An infrared prediction model for orotic acid was built using a training population of 292 Danish Holstein and 299 Danish Jersey cows, and a validation population of 381 Danish Holstein cows. Milk orotic acid concentration was determined with nuclear magnetic resonance spectroscopy. For genetic analysis of infrared orotic acid, 3 study populations were used: 3,210 Danish Holstein cows, 3,360 Danish Jersey cows, and 1,349 Dutch Holstein Friesian cows. Using partial least square regression, a prediction model for orotic acid was built with 18 latent variables. The error of the prediction for the infrared model varied from 1.0 to 3.2 mg/L, and the accuracy varied from 0.68 to 0.86. Heritability of infrared orotic acid predicted with the standardized prediction model was 0.18 for Danish Holstein, 0.09 for Danish Jersey, and 0.37 for Dutch Holstein Friesian. We conclude that milk orotic acid can be predicted with moderate to good accuracy based on infrared milk spectra and that infrared-predicted orotic acid is heritable. The availability of a cheap and fast method to predict milk orotic acid opens up possibilities to study the largely unknown functions of milk orotic acid.

Energy profiling of dairy cows from routine milk mid-infrared analysis

The balance of body energy within and across lactations can have health and fertility consequences for the dairy cow. This study aimed to create a large calibration data set of dairy cow body energy traits across the cow's productive life, with concurrent milk mid-infrared (MIR) spectral data, to generate a prediction tool for use in commercial dairy herds. Detailed phenotypic data from 1,101 Holstein Friesian cows from the Langhill research herd (SRUC, Scotland) were used to generate energy balance (EB) and effective energy intake (EI), both in megajoules per day. Pretreatment of spectral data involved standardization to account for drift over time and machine. Body energy estimates were aligned with their spectral data to generate a prediction of these traits based on milk MIR spectroscopy. After data edits, partial least squares analysis generated prediction equations with a coefficient of determination from split sample 10-fold cross validation of 0.77 and 0.75 for EB and EI, respectively. These prediction equations were applied to national milk MIR spectra on over 11 million animal test dates (January 2013 to December 2016) from 4,453 farms. The predictions generated from these were subject to phenotypic analyses with a fixed regression model highlighting differences between the main dairy breeds in terms of energy traits. Genetic analyses generated heritability estimates for EB and EI ranging from 0.12 to 0.17 and 0.13 to 0.15, respectively. This study shows that MIR-based predictions from routinely collected national data can be used to generate predictions of dairy cow energy turnover profiles for both animal management and genetic improvement of such difficult and expensive-to-record traits.

Persistence of differences between dairy cows categorized as low or high methane emitters, as estimated from milk mid-infrared spectra and measured by GreenFeed

Currently, various attempts are being made to implement breeding schemes aimed at producing low methane (CH₄) emitting cows. We investigated the persistence of differences in CH₄ emission between groups of cows categorized as either low or high emitters over a 5-mo period. Two feeding regimens (pasture vs. indoors) were used. Early- to mid-lactation Holstein Friesian cows were categorized as low or high emitters (n = 10 each) retrospectively, using predictions from milk mid-infrared (MIR) spectra, before the start of the experiment. Data from MIR estimates and from measurements with the GreenFeed (GF; C-Lock Technology Inc., Rapid City, SD) system over the 5-mo experiment were combined into 7-, 14-, and 28-d periods. Feed intake, eating and ruminating behavior, and ruminal fluid traits were determined in two 7-d measurement periods in the grazing season. The CH₄ emission data were analyzed using a split-plot ANOVA, and the repeatability of each of the applied methods for determining CH₄ emission was calculated. Traits other than CH₄ emission were analyzed for differences between low and high emitters using a linear mixed model. The initial category-dependent differences in daily CH₄ production persisted over the subsequent 5 mo and across 2 feeding regimens with both methods. The repeatability analysis indicated that the biweekly milk control scheme, and even a monthly scheme as practiced on farms, might be sufficient for confirming category differences. However, the relationship between CH₄ data estimated by MIR and measured with GF for individual cows was weak (R² = 0.26). The categorization based on CH₄ production also generated differences in CH₄ emission per kilogram of milk; differentiation between cow categories was not persistent based on milk MIR spectra and GF. Compared with the high emitters, low emitters tended to show a lower acetate-to-propionate ratio in ruminal volatile fatty acids, whereas feed intake and ruminating time did not differ. Interestingly, the low emitters spent less time eating than the high emitters. In conclusion, the CH₄ estimation from analyzing the milk MIR spectra is an appropriate proxy to form and regularly control categories of cows with different CH₄ production levels. The categorization was also sufficient to secure similar and persistent differences in emission intensity when estimated by MIR spectra of the milk. Further studies are needed to determine whether MIR data from individual cows are sufficiently accurate for breeding.

Prediction of blood metabolites from milk mid-infrared spectra in early-lactation cows

Dairy cows commonly experience an unbalanced energy status in early lactation, and this condition can lead to the onset of several metabolic disorders. Blood metabolic profile testing is a valid tool to monitor and detect the most common early lactation disorders, but blood sampling and analysis are time-consuming and expensive, and the procedure is invasive and stressful for the cows. Mid-infrared (MIR) spectroscopy is routinely used to analyze milk composition, being a cost-effective and nondestructive method. The present study aimed to assess the feasibility of using routine milk MIR spectra for the prediction of main blood metabolites in dairy cows, and to investigate associations between measured blood metabolites and milk traits. Twenty herds of Holstein Friesian, Brown Swiss, or Simmental cows located in Northeast Italy were visited 1 to 4 times between December 2017 and June 2018, and blood and milk samples were collected from all lactating cows within 35 d in milk. Concentrations of main blood metabolites and milk MIR spectra were recorded from 295 blood and milk samples and used to develop prediction models for blood metabolic traits through backward interval partial least squares analysis. Blood β-hydroxybutyrate (BHB), urea, and nonesterified fatty acids were the most predictable traits, with coefficients of determination of 0.63, 0.58, and 0.52, respectively. On the contrary, predictive performance for blood glucose, triglycerides, cholesterol, glutamic oxaloacetic transaminase, and glutamic pyruvic transaminase were not accurate. Associations of blood BHB and urea with their respective contents in milk were moderate to strong, whereas all other correlations were weak. Predicted blood BHB showed an improved performance in detecting cows with hyperketonemia (blood BHB ≥ 1.2 mmol/L), compared with commercial calibration equation for milk BHB. Results highlighted the opportunity of using milk MIR spectra to predict blood metabolites and thus to collect routine information on the metabolic status of early-lactation cows at a population level.

Classifying the fertility of dairy cows using milk mid-infrared spectroscopy

The objective of this study was to investigate the potential of milk mid-infrared (MIR) spectroscopy, MIR-derived traits including milk composition, milk fatty acids, and blood metabolic profiles (fatty acids, β-hydroxybutyrate, and urea), and other on-farm data for discriminating cows of good versus poor likelihood of conception to first insemination (i.e., pregnant vs. open). A total of 6,488 spectral and milk production records of 2,987 cows from 19 commercial dairy herds across 3 Australian states were used. Seven models, comprising different explanatory variables, were examined. Model 1 included milk production; concentrations of fat, protein, and lactose; somatic cell count; age at calving; days in milk at herd test; and days from calving to insemination. Model 2 included, in addition to the variables in model 1, milk fatty acids and blood metabolic profiles. The MIR spectrum collected before first insemination was added to model 2 to form model 3. Fat, protein, and lactose percentages, milk fatty acids, and blood metabolic profiles were removed from model 3 to create model 4. Model 5 and model 6 comprised model 4 and either fertility genomic estimated breeding value or principal components obtained from a genomic relationship matrix derived using animal genotypes, respectively. In model 7, all previously described sources of information, but not MIR-derived traits, were used. The models were developed using partial least squares discriminant analysis. The performance of each model was evaluated in 2 ways: 10-fold random cross-validation and herd-by-herd external validation. The accuracy measures were sensitivity (i.e., the proportion of pregnant cows that were correctly classified), specificity (i.e., the proportion of open cows that were correctly classified), and area under the curve (AUC) for the receiver operating curve. The results showed that in all models, prediction accuracy obtained through 10-fold random cross-validation was higher than that of herd-by-herd external validation, with the difference in AUC ranging between 0.01 and 0.09. In the herd-by-herd external validation, using basic on-farm information (model 1) was not sufficient to classify good- and poor-fertility cows; the sensitivity, specificity, and AUC were around 0.66. Compared with model 1, adding milk fatty acids and blood metabolic profiles (model 2) increased the sensitivity, specificity, and AUC by 0.01, 0.02, and 0.02 unit, respectively (i.e., 0.65, 0.63, and 0.678). Incorporating MIR spectra into model 2 resulted in sensitivity, specificity, and AUC values of 0.73, 0.63, and 0.72, respectively (model 3). The comparable prediction accuracies observed for models 3 and 4 mean that useful information from MIR-derived traits is already included in the spectra. Adding the fertility genomic estimated breeding value and animal genotypes (model 7) produced the highest prediction accuracy, with sensitivity, specificity, and AUC values of 0.75, 0.66, and 0.75, respectively. However, removing either the fertility estimated breeding value or animal genotype from model 7 resulted in a reduction of the prediction accuracy of only 0.01 and 0.02, respectively. In conclusion, this study indicates that MIR and other on-farm data could be used to classify cows of good and poor likelihood of conception with promising accuracy.

Comparison of Bayesian and partial least squares regression methods for mid-infrared prediction of cheese-making properties in Montbéliarde cows

Assessing the cheese-making properties (CMP) of milks with a rapid and cost-effective method is of particular interest for the Protected Designation of Origin cheese sector. The aims of this study were to evaluate the potential of mid-infrared (MIR) spectra to estimate coagulation and acidification properties, as well as curd yield (CY) traits of Montbéliarde cow milk. Samples from 250 cows were collected in 216 commercial herds in Franche-Comté with the objectives to maximize the genetic diversity as well as the variation in milk composition. All coagulation and CY traits showed high variability (10 to 43%). Reference analyses performed for soft (SC) and pressed cooked (PCC) cheese technology were matched with MIR spectra. Prediction models were built on 446 informative wavelengths not tainted by the water absorbance, using different approaches such as partial least squares (PLS), uninformative variable elimination PLS, random forest PLS, Bayes A, Bayes B, Bayes C, and Bayes RR. We assessed equation performances for a set of 20 CMP traits (coagulation: 5 for SC and 4 for PCC; acidification: 5 for SC and 3 for PCC; laboratory CY: 3) by comparing prediction accuracies based on cross-validation. Overall, variable selection before PLS did not significantly improve the performances of the PLS regression, the prediction differences between Bayesian methods were negligible, and PLS models always outperformed Bayesian models. This was likely a result of the prior use of informative wavelengths of the MIR spectra. The best accuracies were obtained for curd yields expressed in dry matter (CY_DM) or fresh (CY_FRESH) and for coagulation traits (curd firmness for PCC and SC) using the PLS regression. Prediction models of other CMP traits were moderately to poorly accurate. Whatever the prediction methodology, the best results were always obtained for CY traits, probably because these traits are closely related to milk composition. The CY_DM predictions showed coefficient of determination (R²) values up to 0.92 and 0.87, and RS_y,x values of 3 and 4% for PLS and Bayes regressions, respectively. Finally, we divided the data set into calibration (2/3) and validation (1/3) sets and developed prediction models in external validation using PLS regression only. In conclusion, we confirmed, in the validation set, an excellent prediction for CY_DM [R² = 0.91, ratio of performance to deviation (RPD) = 3.39] and a very good prediction for CY_FRESH (R² = 0.84, RPD = 2.49), adequate for analytical purposes. We also obtained good results for both PCC and SC curd firmness traits (R² ≥ 0.70, RPD ≥1.8), which enable quantitative prediction.

The use of mid-infrared spectra to map genes affecting milk composition

The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk samples to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on individual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.

Validation strategy can result in an overoptimistic view of the ability of milk infrared spectra to predict methane emission of dairy cattle

Because of the environmental impact of methane (CH₄), it is of great interest to reduce CH₄ emission of dairy cattle and selective breeding might contribute to this. However, this approach requires a rapid and inexpensive measurement technique that can be used to quantify CH₄ emission for a large number of individual dairy cows. Milk infrared (IR) spectroscopy has been proposed as a predictor for CH₄ emission. In this study, we investigated the feasibility of milk IR spectra to predict breath sensor-measured CH₄ of 801 dairy cows on 10 commercial farms. To evaluate the prediction equation, we used random and block cross validation. Using random cross validation, we found a validation coefficient of determination (R²val) of 0.49, which suggests that milk IR spectra are informative in predicting CH₄ emission. However, based on block cross validation, with farms as blocks, a negligible R²val of 0.01 was obtained, indicating that milk IR spectra cannot be used to predict CH₄ emission. Random cross validation thus results in an overoptimistic view of the ability of milk IR spectra to predict CH₄ emission of dairy cows. The difference between the validation strategies could be due to the confounding of farm and date of milk IR analysis, which introduces a correlation between batch effects on the IR analyses and farm-average CH₄. Breath sensor-measured CH₄ is strongly influenced by farm-specific conditions, which magnifies the problem. Milk IR wavenumbers from water absorption regions, which are generally considered uninformative, showed moderate accuracy (R²val = 0.25) when based on random cross validation, but not when based on block cross validation (R²val = 0.03). These results indicate, therefore, that in the current study, random cross validation results in an overoptimistic view on the ability of milk IR spectra to predict CH₄ emission. We suggest prediction based on wavenumbers from water absorption regions as a negative control to identify potential dependence structures in the data.

Strategies for noise reduction and standardization of milk mid-infrared spectra from dairy cattle

The use of Fourier-transform mid-infrared (FTIR) spectroscopy is of interest to the dairy industry worldwide for predicting milk composition and other novel traits that are difficult or expensive to measure directly. Although there are many valuable applications for FTIR spectra, noise from differences in spectral responses between instruments is problematic because it reduces prediction accuracy if ignored. The purpose of this study was to develop strategies to reduce the impact of noise and to compare methods for standardizing FTIR spectra in order to reduce between-instrument variability in multiple-instrument networks. Noise levels in bands of the infrared spectrum caused by the water content of milk were characterized, and a method for identifying and removing outliers was developed. Two standardization methods were assessed and compared: piecewise direct standardization (PDS), which related spectra on a primary instrument to spectra on 5 other (secondary) instruments using identical milk-based reference samples (n = 918) analyzed across the 6 instruments; and retroactive percentile standardization (RPS), whereby percentiles of observed spectra from routine milk test samples (n = 2,044,094) were used to map and exploit primary- and secondary-instrument relationships. Different applications of each method were studied to determine the optimal way to implement each method across time. Industry-standard predictions of milk components from 2,044,094 spectra records were regressed against predictions from spectra before and after standardization using PDS or RPS. The PDS approach resulted in an overall decrease in root mean square error between industry-standard predictions and predictions from spectra from 0.190 to 0.071 g/100 mL for fat, from 0.129 to 0.055 g/100 mL for protein, and from 0.143 to 0.088 g/100 mL for lactose. Reductions in prediction error for RPS were similar but less consistent than those for PDS across time, but similar reductions were achieved when PDS coefficients were updated monthly and separate primary instruments were assigned for the North and South Islands of New Zealand. We demonstrated that the PDS approach is the most consistent method to reduce prediction errors across time. We also showed that the RPS approach is sensitive to shifts in milk composition but can be used to reduce prediction errors, provided that secondary-instrument spectra are standardized to a primary instrument with samples of broadly equivalent milk composition. Appropriate implementation of either of these approaches will improve the quality of predictions based on FTIR spectra for various downstream applications.

Variation of Detailed Protein Composition of Cow Milk Predicted from a Large Database of Mid-Infrared Spectra

Simple Summary

Milk proteins are one of the most valuable milk components. The objective of the present study was to assess sources of variation of detailed protein composition predicted from infrared spectra in milk of dairy and dual-purpose cattle breeds. Results showed that protein fractions were primarily influenced by days in milk, and the relative proportion of each fraction through lactation was not constant. Protein fractions correlated with crude protein, total casein, fat and milk urea nitrogen. In perspective, mid-infrared predictions of milk fractions could be useful for the dairy sector to improve nutritional and technological properties of milk.

Abstract

This study aimed to investigate factors affecting protein fractions, namely α-casein (α-CN), β-casein (β-CN), κ-casein (κ-CN), β-lactoglobulin (β-LG) and α-lactalbumin (α-LA) predicted from milk infrared spectra in milk of dairy and dual-purpose cattle breeds. The dataset comprised 735,328 observations from 49,049 cows in 1782 herds. Results highlighted significant differences of protein fractions in milk of the studied breeds. Significant variations of protein fractions were found also through parities and lactation, with the latter thoroughly influencing protein fractions percentage. Interesting correlations (r) were estimated between β-CN, κ-CN and β-LG, expressed as percentage of crude protein, and milk urea nitrogen (r = 0.31, −0.20 and −0.26, respectively) and between α-LA and fat percentage (r = 0.41). The present study paves the way for future studies on the associations between protein fractions and milk technological properties, and for the estimation of genetic parameters of predicted protein composition.

Symposium review: Challenges and opportunities for evaluating and using the genetic potential of dairy cattle in the new era of sensor data from automation

Sensor data from automation are becoming available on an increasingly large scale, and associated research is slowly starting to appear. This new era of sensor data from automation leads to many challenges but also new opportunities for assessing and maximizing the genetic potential of dairy cattle. The first challenge is data quality, because all uses of sensor data require careful data quality validation, potentially using external references. The second issue is data accessibility. Indeed, sensor data generated from automation are often designed to be available on-farm in a given system. However, to make these data useful-for genetic improvement for example-the data must also be made available off-farm. By nature, sensor data often are very complex and diverse; therefore, a data consolidation and integration layer is required. Moreover, the traits we want to select have to be defined precisely when generated from these raw data. This approach is obviously also beneficial to limit the challenge of extremely high data volumes generated by sensors. An additional challenge is that sensors will always be deployed in a context of herd management; therefore, any efforts to make them useful should focus on both breeding and management. However, this challenge also leads to opportunities to use genomic predictions based on these novel data for breeding and management. Access to relevant phenotypes is crucial for every genomic evaluation system. The automatic generation of training data, on both the phenotypic and genomic levels, is a major opportunity to access novel, precise, continuously updated, and relevant data. If the challenges of bidirectional data transfer between farms and external databases can be solved, new opportunities for continuous genomic evaluations integrating genotypes and the most current local phenotypes can be expected to appear. Novel concepts such as federated learning may help to limit exchange of raw data and, therefore, data ownership issues, which is another important element limiting access to sensor data. Accurate genome-guided decision-making and genome-guided management of dairy cattle should be the ultimate way to add value to sensor data from automation. This could also be the major driving force to improve the cost-benefit relationship for sensor-based technologies, which is currently one of the major obstacles for large-scale use of available technologies.

Long-Term Strategy for Assessing Carbonaceous Particulate Matter Concentrations from Multiple Fourier Transform Infrared (FT-IR) Instruments: Influence of Spectral Dissimilarities on Multivariate Calibration Performance

Matching the spectral response between multiple spectrometers is a mandatory procedure when developing robust calibrations whose prediction is independent of instrument-related signal variations. A viable alternative to complex calibration transfer methods consists of matching the instrument spectral response by controlling a set of key instrumental and environmental parameters. This paper discusses the applicability of such an approach to three Fourier transform infrared (FT-IR) spectrometers used for the routine assessment of carbonaceous particulate matter concentrations in the Interagency Monitoring of PROtected Visual Environments (IMPROVE) speciation network. The effectiveness of the proposed matching procedure is evaluated by comparing the spectral response for each individual instrument in order to characterize the extent, and nature, of the remaining inter-instrument spectral dissimilarities. Instrument-related contributions to the signal were determined to be small compared with the spectral variability induced by the filter type used for sample collection. The impact of spectral differences on prediction was addressed through the comparison of model performance derived from multiple calibration scenarios. A hybrid model yielding accurate and homogeneous prediction regardless of the instrument was proposed for organic carbon (OC) and elemental carbon (EC), two major constituents of atmospheric particulate matter. Coefficients of determination of 0.98 (OC) and 0.90 (EC) with median biases not exceeding 0.20 µg (OC) and 0.07 µg (EC) are reported. The long-term stability, assessed from weekly measurements of reference samples, shows a deviation in predicted concentrations of less than ±5% over a 2.5-year period for most of the data collected. Extending OC and EC hybrid models to the prediction of ambient samples collected during the two subsequent years provides satisfactory performance. The proposed instrument matching procedure coupled with the relative simplicity of the hybrid model is an alternative to computationally advanced calibration transfer methodologies for the characterization of carbonaceous particulate matter using multiple FT-IR instruments.

Prediction of metabolic clusters in early-lactation dairy cows using models based on milk biomarkers

The aim of this study was to describe metabolism of early-lactation dairy cows by clustering cows based on glucose, insulin-like growth factor I (IGF-I), free fatty acid, and β-hydroxybutyrate (BHB) using the k-means method. Predictive models for metabolic clusters were created and validated using 3 sets of milk biomarkers (milk metabolites and enzymes, glycans on the immunogamma globulin fraction of milk, and Fourier-transform mid-infrared spectra of milk). Metabolic clusters are used to identify dairy cows with a balanced or imbalanced metabolic profile. Around 14 and 35 d in milk, serum or plasma concentrations of BHB, free fatty acids, glucose, and IGF-I were determined. Cows with a favorable metabolic profile were grouped together in what was referred to as the "balanced" group (n = 43) and were compared with cows in what was referred to as the "other balanced" group (n = 64). Cows with an unfavorable metabolic profile were grouped in what was referred to as the "imbalanced" group (n = 19) and compared with cows in what was referred to as the "other imbalanced" group (n = 88). Glucose and IGF-I were higher in balanced compared with other balanced cows. Free fatty acids and BHB were lower in balanced compared with other balanced cows. Glucose and IGF-I were lower in imbalanced compared with other imbalanced cows. Free fatty acids and BHB were higher in imbalanced cows. Metabolic clusters were related to production parameters. There was a trend for a higher daily increase in fat- and protein-corrected milk yield in balanced cows, whereas that of imbalanced cows was higher. Dry matter intake and the daily increase in dry matter intake were higher in balanced cows and lower in imbalanced cows. Energy balance was continuously higher in balanced cows and lower in imbalanced cows. Weekly or twice-weekly milk samples were taken and milk metabolites and enzymes (milk glucose, glucose-6-phosphate, BHB, lactate dehydrogenase, N-acetyl-β-d-glucosaminidase, isocitrate), immunogamma globulin glycans (19 peaks), and Fourier-transform mid-infrared spectra (1,060 wavelengths reduced to 15 principal components) were determined. Milk biomarkers with or without additional cow information (days in milk, parity, milk yield features) were used to create predictive models for the metabolic clusters. Accuracy for prediction of balanced (80%) and imbalanced (88%) cows was highest using milk metabolites and enzymes combined with days in milk and parity. The results and models of the present study are part of the GplusE project and identify novel milk-based phenotypes that may be used as predictors for metabolic and performance traits in early-lactation dairy cows.

Potential of milk mid-IR spectra to predict metabolic status of cows through blood components and an innovative clustering approach

Unbalanced metabolic status in the weeks after calving predisposes dairy cows to metabolic and infectious diseases. Blood glucose, IGF-I, non-esterified fatty acids (NEFA) and β-hydroxybutyrate (BHB) are used as indicators of the metabolic status of cows. This work aims to (1) evaluate the potential of milk mid-IR spectra to predict these blood components individually and (2) to evaluate the possibility of predicting the metabolic status of cows based on the clustering of these blood components. Blood samples were collected from 241 Holstein cows on six experimental farms, at days 14 and 35 after calving. Blood samples were analyzed by reference analysis and metabolic status was defined by k-means clustering (k=3) based on the four blood components. Milk mid-IR analyses were undertaken on different instruments and the spectra were harmonized into a common standardized format. Quantitative models predicting blood components were developed using partial least squares regression and discriminant models aiming to differentiate the metabolic status were developed with partial least squares discriminant analysis. Cross-validations were performed for both quantitative and discriminant models using four subsets randomly constituted. Blood glucose, IGF-I, NEFA and BHB were predicted with respective R 2 of calibration of 0.55, 0.69, 0.49 and 0.77, and R 2 of cross-validation of 0.44, 0.61, 0.39 and 0.70. Although these models were not able to provide precise quantitative values, they allow for screening of individual milk samples for high or low values. The clustering methodology led to the sharing out of the data set into three groups of cows representing healthy, moderately impacted and imbalanced metabolic status. The discriminant models allow to fairly classify the three groups, with a global percentage of correct classification up to 74%. When discriminating the cows with imbalanced metabolic status from cows with healthy and moderately impacted metabolic status, the models were able to distinguish imbalanced group with a global percentage of correct classification up to 92%. The performances were satisfactory considering the variables are not present in milk, and consequently predicted indirectly. This work showed the potential of milk mid-IR analysis to provide new metabolic status indicators based on individual blood components or a combination of these variables into a global status. Models have been developed within a standardized spectral format, and although robustness should preferably be improved with additional data integrating different geographic regions, diets and breeds, they constitute rapid, cost-effective and large-scale tools for management and breeding of dairy cows.

Consequences of genetic selection for environmental impact traits on economically important traits in dairy cows

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits.

Standardization of milk mid-infrared spectrometers for the transfer and use of multiple models

An increasing number of models are being developed to provide information from milk Fourier transform mid-infrared (FT-MIR) spectra on fine milk composition, technological properties of milk, or even cows' physiological status. In this context, and to take advantage of these existing models, the purpose of this work was to evaluate whether a spectral standardization method can enable the use of multiple equations within a network of different FT-MIR spectrometers. The piecewise direct standardization method was used, matching "slave" instruments to a common reference, the "master." The effect of standardization on network reproducibility was assessed on 66 instruments from 3 different brands by comparing the spectral variability of the slaves and the master with and without standardization. With standardization, the global Mahalanobis distance from the slave spectra to the master spectra was reduced on average from 2,655.9 to 14.3, representing a significant reduction of noninformative spectral variability. The transfer of models from instrument to instrument was tested using 3 FT-MIR models predicting (1) the quantity of daily methane emitted by dairy cows, (2) the concentration of polyunsaturated fatty acids in milk, and (3) the fresh cheese yield. The differences, in terms of root mean squared error, between master predictions and slave predictions were reduced after standardization on average from 103 to 17 g/d, from 0.0315 to 0.0045 g/100 mL of milk, and from 2.55 to 0.49 g of curd/100 g of milk, respectively. For all the models, standard deviations of predictions among all the instruments were also reduced by 5.11 times for methane, 5.01 times for polyunsaturated fatty acids, and 7.05 times for fresh cheese yield, showing an improvement of prediction reproducibility within the network. Regarding the results obtained, spectral standardization allows the transfer and use of multiple models on all instruments as well as the improvement of spectral and prediction reproducibility within the network. The method makes the models universal, thereby offering opportunities for data exchange and the creation and use of common robust models at an international level to provide more information to the dairy sector from direct analysis of milk.

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

The objective of this study was to compare the prediction accuracy of 92 infrared prediction equations obtained by different statistical approaches. The predicted traits included fatty acid composition (n = 1,040); detailed protein composition (n = 1,137); lactoferrin (n = 558); pH and coagulation properties (n = 1,296); curd yield and composition obtained by a micro-cheese making procedure (n = 1,177); and Ca, P, Mg, and K contents (n = 689). The statistical methods used to develop the prediction equations were partial least squares regression (PLSR), Bayesian ridge regression, Bayes A, Bayes B, Bayes C, and Bayesian least absolute shrinkage and selection operator. Model performances were assessed, for each trait and model, in training and validation sets over 10 replicates. In validation sets, Bayesian regression models performed significantly better than PLSR for the prediction of 33 out of 92 traits, especially fatty acids, whereas they yielded a significantly lower prediction accuracy than PLSR in the prediction of 8 traits: the percentage of C18:1n-7 trans-9 in fat; the content of unglycosylated κ-casein and its percentage in protein; the content of α-lactalbumin; the percentage of α_S2-casein in protein; and the contents of Ca, P, and Mg. Even though Bayesian methods produced a significant enhancement of model accuracy in many traits compared with PLSR, most variations in the coefficient of determination in validation sets were smaller than 1 percentage point. Over traits, the highest predictive ability was obtained by Bayes C even though most of the significant differences in accuracy between Bayesian regression models were negligible.

Capitalizing on fine milk composition for breeding and management of dairy cows

The challenge of managing and breeding dairy cows is permanently adapting to changing production circumstances under socio-economic constraints. If managing and breeding address different timeframes of action, both need relevant phenotypes that allow for precise monitoring of the status of the cows, and their health, behavior, and well-being as well as their environmental impact and the quality of their products (i.e., milk and subsequently dairy products). Milk composition has been identified as an important source of information because it could reflect, at least partially, all these elements. Major conventional milk components such as fat, protein, urea, and lactose contents are routinely predicted by mid-infrared (MIR) spectrometry and have been widely used for these purposes. But, milk composition is much more complex and other nonconventional milk components, potentially predicted by MIR, might be informative. Such new milk-based phenotypes should be considered given that they are cheap, rapidly obtained, usable on a large scale, robust, and reliable. In a first approach, new phenotypes can be predicted from MIR spectra using techniques based on classical prediction equations. This method was used successfully for many novel traits (e.g., fatty acids, lactoferrin, minerals, milk technological properties, citrate) that can be then useful for management and breeding purposes. An innovation was to consider the longitudinal nature of the relationship between the trait of interest and the MIR spectra (e.g., to predict methane from MIR). By avoiding intermediate steps, prediction errors can be minimized when traits of interest (e.g., methane, energy balance, ketosis) are predicted directly from MIR spectra. In a second approach, research is ongoing to detect and exploit patterns in an innovative manner, by comparing observed with expected MIR spectra directly (e.g., pregnancy). All of these traits can then be used to define best practices, adjust feeding and health management, improve animal welfare, improve milk quality, and mitigate environmental impact. Under the condition that MIR data are available on a large scale, phenotypes for these traits will allow genetic and genomic evaluations. Introduction of novel traits into the breeding objectives will need additional research to clarify socio-economic weights and genetic correlations with other traits of interest.