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

Standardization method, testing scenario, and accuracy of the infrared prediction model affect the standardization accuracy of milk mid-infrared spectra

The widespread use of milk mid-infrared (MIR) spectroscopy for phenotype prediction has urged the application of prediction models across regions and countries. Spectra standardization is the most effective way to reduce the variability in the spectral signal provided by different instruments and labs. This study aimed to develop different standardization models for MIR spectra collected by multiple instruments, across 2 provinces of China, and investigate whether the standardization method (piecewise direct standardization, PDS, and direct standardization, DS), testing scenario (standardization of spectra collected on the same day or after 7 mo), infrared prediction model accuracy (high or low), and instrument (6 instruments from 2 brands) affect the performance of the standardization model. The results showed that the determination coefficient (R2) between absorbance values at each wavenumber provided by the primary and the secondary instruments increased from less than 0.90 to nearly 1.00 after standardization. Both PDS and DS successfully reduced spectra variation among instruments, and performed significantly better than nonstandardization. However, DS was more prone to overfitting than PDS. Standardization accuracy was higher when tested using spectra collected on the same day compared with those collected 7 mo after, but great improvement in model transferability was obtained for both scenarios compared with the nonstandardized spectra. The less accurate infrared prediction model (for C8:0 and C10:0 content) benefited the most from spectra standardization compared with the more accurate model (for total fat and protein content). For spectra collected 7 mo after standardization, after PDS the root mean square error between predictions obtained by different machines decreased on average by 86% and 94% compared with the values before standardization for C8:0 and C10:0, respectively. The secondary instrument had no significant effect on the R2 between predictions. The variation in the spectral signal provided by different instruments was successfully reduced by standardization across 2 provinces in China. This study lays the foundations for developing a national MIR spectra database to provide consistent predictions across provinces to be used in dairy farm management and breeding programs in China. Additionally, this provides opportunities for data exchange and cooperation at international levels.

Transferability across countries of equations developed using milk mid-infrared spectroscopy to estimate daily body condition score change in dairy cows

Routine milk samples are commonly subjected to spectroscopic analysis within the mid-infrared (MIR) region of the electromagnetic spectrum to estimate macro-constituents of milk like fat, protein, lactose, and urea content. These spectra, however, can also be used to predict other traits, such as daily body condition score (BCS) change. The objective of the present study was to assess the transferability across countries of equations to predict daily body condition score change (ΔBCS) developed using milk MIR data collected in Ireland and in Canada. Body condition was scored on a scale from 1 (emaciated) to 5 (obese) in both countries. A total of 347,254 BCS records from 80,400 Canadian cows were available along with 73,193 BCS records from 6,572 Irish cows. Partial least squares regression (PLSR) and neural networks (NN) were separately used to predict daily ΔBCS. Two scenarios were studied 1) using Canadian and Irish data combined as the calibration data set to predict daily ΔBCS in Canada and in Ireland separately, and 2) Canadian and Irish data used separately to predict daily ΔBCS in each country separately. These prediction methods were applied to data with and without pretreatment (i.e., first derivative of the spectrum) as well as with and without standardizing daily ΔBCS across countries. For all the scenarios investigated, the correlation between actual and predicted daily ΔBCS when calibrated and validated (using cross-validation) in the same country ranged from 0.92 to 0.94, and from 0.85 to 0.87 for the Canadian and Irish data sets, respectively. When the data from Canada and Ireland were combined in the calibration process to predict daily ΔBCS, the correlations between actual and predicted ΔBCS were ≥ 0.90 and ≥ 0.80 for Canadian and Irish daily ΔBCS, respectively indicating no improvement in predictive ability. Predictive performance when calibrated using just Canadian data and validated using just Irish data was poor, and vice versa. Nonetheless, when developing equations for a country for which a limited database (i.e., 100 records) of gold standard and MIR data were available, predictive performance improved when the limited database was supplemented with the large data set from the other country. In general, for some of the investigated scenarios, standardizing the daily ΔBCS data within country before undertaking the calibration improved prediction accuracy. In conclusion, the benefit of merging data from different countries, at least based on the trait (i.e., daily ΔBCS) and countries (i.e., Ireland and Canada) considered in the present study were limited and, in cases, counter-productive.

Using milk mid-infrared spectroscopy to estimate cow-level nitrogen efficiency metrics

Minimizing pollution from the dairy sector is paramount; one potential cause of such pollution is excess nitrogen. Nitrogen pollution contributes to a deterioration in water quality as well as an increase in both eutrophication and greenhouse gases. It is therefore essential to minimize the loss of nitrogen from the sector, including excretion from the cow. Breeding programs are one potential strategy to improve the efficiency with which nitrogen is used by dairy cows, but they rely on routine access to individual cow information on how efficiently each cow uses the nitrogen it ingests. A total of 3,497 test-day records for individual-cow nitrogen efficiency metrics along with milk yield and the associated milk spectra were used to investigate the ability of milk infrared spectral data to predict these nitrogen traits; both traditional partial least squares regression and neural networks were used in the prediction process. The data originated from 4 farms across 11 yr. The nitrogen traits investigated were nitrogen intake, nitrogen use efficiency, and nitrogen balance. Both nitrogen use efficiency and nitrogen balance were calculated considering nitrogen intake, nitrogen in milk, nitrogen in the conceptus, nitrogen used for the growth, nitrogen stored in body reserves, and nitrogen mobilized from body reserves. Irrespective of the nitrogen-related trait being investigated, the best predictions from 4-fold cross validation were achieved using neural networks that considered both the morning and evening milk spectra along with milk yield, parity, and DIM in the prediction process. The coefficient of determination in the cross validation was 0.61, 0.74, and 0.58 for nitrogen intake, nitrogen use efficiency, and nitrogen balance, respectively. In a separate series of validation approaches, the calibration and validation was stratified by herd (n = 4) and separately by year. For these scenarios, partial least squares regression generated more accurate predictions compared with neural networks; the coefficient of determination was always lower than 0.29 and 0.60 when validation was stratified by herd and year, respectively. Therefore, if the variability of the data being predicted in the validation datasets is similar to that in the data used to develop the predictions, then nitrogen-related traits can be predicted with reasonable accuracy. In contrast, where the variability of the data that exists in the validation dataset is poorly represented in the calibration dataset, then poor predictions will ensue.

Phenotypic and genomic modeling of lactation curves: A longitudinal perspective

Lactation curves, which describe the production pattern of milk-related traits over time, provide insightful information about individual cow health, resilience, and milk production efficiency. Key functional traits can be derived through lactation curve modeling, such as lactation peak and persistency. Furthermore, novel traits such as resilience indicators can be derived based on the variability of the deviations of observed milk yield from the expected lactation curve fitted for each animal. Lactation curve parameters are heritable, indicating that one can modify the average lactation curve of a population through selective breeding. Various statistical methods can be used for modeling longitudinal traits. Among them, the use of random regression models enables a more flexible and robust modeling of lactation curves compared with traditional models used to evaluate accumulated milk 305-d yield, as they enable the estimation of both genetic and environmental effects affecting milk production traits over time. In this symposium review, we discuss the importance of evaluating lactation curves from a longitudinal perspective and various statistical and mathematical models used to analyze longitudinal data. We also highlighted the key factors that influence milk production over time, and the potential applications of longitudinal analyses of lactation curves in improving animal health, resilience, and milk production efficiency. Overall, analyzing the longitudinal nature of milk yield will continue to play a crucial role in improving the production efficiency and sustainability of the dairy industry, and the methods and models developed can be easily translated to other longitudinal traits.

Genetic covariance components for measures of nitrogen utilization in grazing dairy cows

Improved nitrogen utilization of dairy production systems should improve not only the economic output of the systems but also the environmental metrics. One strategy to improve efficiency is through breeding programs. Improving a trait through breeding is conditional on the presence of exploitable genetic variability. Using a database of 1,291 deeply phenotyped grazing dairy cows, the genetic variability for 2 definitions of nitrogen utilization was studied: nitrogen use efficiency (i.e., nitrogen output in milk and meat divided by nitrogen available) and nitrogen balance (i.e., nitrogen available less nitrogen output in milk and meat). Variance components for both variables were estimated using animal repeatability linear mixed models. Genetic variability was detected for both nitrogen utilization metrics, even though their heritability estimates were low (<0.10). Validation of genetic evaluations revealed that animals divergent for nitrogen use efficiency or nitrogen balance indeed differed phenotypically, further demonstrating that breeding for improved nitrogen efficiency should result in a shift in the population mean toward better efficiency. Nitrogen use efficiency and nitrogen balance were not genetically correlated with each other (<|0.28|), and neither metric was correlated with milk urea nitrogen (<|0.12|). Nitrogen balance was unfavorably correlated with milk yield, showing the importance of including the nitrogen utilization metrics in a breeding index to improve nitrogen utilization without negatively impacting milk yield. In conclusion, improvement of nitrogen utilization through breeding is possible, even if more nitrogen utilization phenotypic data need to be collected to improve the selection accuracy considering the low heritability estimates.

Imputation of missing milk Fourier transform mid-infrared spectra using existing milk spectral databases: A strategy to improve the reliability of breeding values and predictive models

The use of milk Fourier transform mid-infrared (FT-MIR) spectrometry to develop management and breeding tools for dairy farmers and industry is growing and supported by the availability of numerous new predicted phenotypes to assess the nutritional quality of milk and its technological properties, but also the animal health and welfare status and its environmental fingerprint. For genetic evaluations, having a long-term and representative spectral dairy herd improvement (DHI) database improves the reliabilities of estimated breeding values (EBV) from these phenotypes. Unfortunately, most of the time, the raw spectral data used to generate these estimations are not stored. Moreover, many reference measurements of those phenotypes, needed during the FT-MIR calibration step, are available from past research activities but lack spectra records. So, it is impossible to use them to improve the FT-MIR models. Consequently, there is a strong interest in imputing those missing spectra. The innovative objective of this study was to use the existing large spectral DHI database to estimate missing spectra by selecting probable spectra using, as the match criteria, common dairy traits recorded for a long time by DHI organizations. We tested 4 match criteria combinations. Combination 1 required to have equal fat and protein contents between the sample for which a spectrum was to be estimated and the reference samples in the DHI database. Combination 2 also required an equal urea content. Combination 3 requested equal fat, protein, and lactose contents. Finally, combination 4 included all criteria. When more than one spectrum was found during the search, their average was the estimated spectrum for the query sample. Concretely, this study estimated missing spectra for 1,700 samples using 2,000,000 spectral DHI records. For assessing the effect of this spectral estimation on the prediction quality, FT-MIR equations were used to predict 11 phenotypes, selected as their quantification used different FT-MIR regions. They were related to the milk fat and mineral composition, lactoferrin content, quantity of eructed methane, body weight (BW), and dry matter intake. The accuracy between predictions obtained from actual and estimated spectra was evaluated by calculating the mean absolute error (MAE). The criteria in the fourth and second combinations were too strict to estimate a spectrum for most samples. Indeed, for many samples, no spectra with the same values for those matching criteria was found. The third match criteria combination had a poorer prediction performance for all studied traits and spectral absorptions than the first combination due to fewer matched samples available to compute the missing spectrum. By allowing a range for matching lactose content (±0.1 g/dL milk), we showed that this new combination increased the number of selected samples to compute missing spectra and predict better the infrared absorption at different wavenumbers, especially those related to the lactose quantification. The prediction performance was further improved by performing queries on the entire Walloon DHI spectral database (6,625,570 spectra), and it varied among the studied phenotypes. Without considering the traits used for the matching, the best predictions were obtained for the content of saturated fatty acids (MAE = 0.15 g/dL milk) and BW (MAE = 12.80 kg). Yet, the predictions for the unsaturated fatty acids were less accurate (MAE = 0.13 and 0.018 g/dL milk for monounsaturated and polyunsaturated fatty acids), likely because of the poorer predictions of spectral regions related to long-chain fatty acids. Similarly, poorer predictions were observed for the amount of methane eructed by dairy cows (MAE = 47.02 g/d), likely because it is not directly related to fat content or composition. Prediction accuracies for the remaining traits were also low. In conclusion, we observed that increasing the number of relevant matching criteria helps improve the quality of FT-MIR predicted phenotypes and the number of spectra used during the search. So, it would be of great interest to test in the future the suitability of the developed methodology with large-scale international spectral databases to improve the reliability of EBV from these FT-MIR-based phenotypes and the robustness of FT-MIR predictive models.

Microbial signature inferred from genomic breeding selection on milk urea concentration and its relation to proxies of nitrogen-utilization efficiency in Holsteins

Increasing the nitrogen-utilization efficiency (NUE) of dairy cows by breeding selection would offer advantages from nutritional, environmental, and economic perspectives. Because data collection of NUE phenotypes is not feasible in large cow cohorts, the cow individual milk urea concentration (MU) has been suggested as an indicator trait. Considering the symbiotic interplay between dairy cows and their rumen microbiome, individual MU was thought to be influenced by host genetics and by the rumen microbiome, the latter in turn being partly attributed to host genetics. To enhance our knowledge of MU as an indicator trait for NUE, we aimed to identify differential abundant rumen microbial genera between Holstein cows with divergent genomic breeding values for MU (GBVMU; GBV_HMU vs. GBV_LMU, where H and L indicate high and low MU phenotypes, respectively). The microbial genera identified were further investigated for their correlations with MU and 7 additional NUE-associated traits in urine, milk, and feces in 358 lactating Holsteins. Statistical analysis of microbial 16S rRNA amplicon sequencing data revealed significantly higher abundances of the ureolytic genus Succinivibrionaceae UCG-002 in GBV_LMU cows, whereas GBV_HMU animals hosted higher abundances of Clostridia unclassified and Desulfovibrio. The entire discriminating ruminal signature of 24 microbial taxa included a further 3 genera of the Lachnospiraceae family that revealed significant correlations to MU values and were therefore proposed as considerable players in the GBVMU-microbiome-MU axis. The significant correlations of Prevotellaceae UCG-003, Anaerovibrio, Blautia, and Butyrivibrio abundances with MU measurements, milk nitrogen, and N content in feces suggested their contribution to genetically determined N-utilization in Holstein cows. The microbial genera identified might be considered for future breeding programs to enhance NUE in dairy herds.

Genome-wide association study and functional annotation analyses for nitrogen efficiency index and its composition traits in dairy cattle

The aims of this study were (1) to identify genomic regions associated with a N efficiency index (NEI) and its composition traits and (2) to analyze the functional annotation of identified genomic regions. The NEI included N intake (NINT1), milk true protein N (MTPN1), milk urea N yield (MUNY1) in primiparous cattle, and N intake (NINT2+), milk true protein N (MTPN2+), and milk urea N yield (MUNY2+) in multiparous cattle (2 to 5 parities). The edited data included 1,043,171 records on 342,847 cows distributed in 1,931 herds. The pedigree consisted of 505,125 animals (17,797 males). Data of 565,049 SNPs were available for 6,998 animals included in the pedigree (5,251 females and 1,747 males). The SNP effects were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of about 240 kb) was calculated. The top 3 genomic regions explaining the largest rate of the total additive genetic variance of the NEI and its composition traits were selected for candidate gene identification and quantitative trait loci (QTL) annotation. The selected genomic regions explained from 0.17% (MTPN2+) to 0.58% (NEI) of the total additive genetic variance. The largest explanatory genomic regions of NEI, NINT1, NINT2+, MTPN1, MTPN2+, MUNY1, and MUNY2+ were Bos taurus autosome 14 (1.52-2.09 Mb), 26 (9.24-9.66 Mb), 16 (75.41-75.51 Mb), 6 (8.73-88.92 Mb), 6 (8.73-88.92 Mb), 11 (103.26-103.41 Mb), 11 (103.26-103.41 Mb). Based on the literature, gene ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction, 16 key candidate genes were identified for NEI and its composition traits, which are mainly expressed in the milk cell, mammary, and liver tissues. The number of enriched QTL related to NEI, NINT1, NINT2+, MTPN1, and MTPN2+ were 41, 6, 4, 11, 36, 32, and 32, respectively, and most of them were related to the milk, health, and production classes. In conclusion, this study identified genomic regions associated with NEI and its composition traits, and identified key candidate genes describing the genetic mechanisms of N use efficiency-related traits. Furthermore, the NEI reflects not only its composition traits but also the interactions among them.

Using machine learning methods to predict dry matter intake from milk mid-infrared spectroscopy data on Swedish dairy cattle

In this research communication we compare three different approaches for developing dry matter intake (DMI) prediction models based on milk mid-infrared spectra (MIRS), using data collected from a research herd over five years. In dairy production, knowledge of individual DMI could be important and useful, but DMI can be difficult and expensive to measure on most commercial farms as cows are commonly group-fed. Instead, this parameter is often estimated based on the age, body weight, stage of lactation and body condition score of the cow. Recently, milk MIRS have also been used as a tool to estimate DMI. There are different methods available to create prediction models from large datasets. The main data used were total DMI calculated as a 3-d average, coupled with milk MIRS data available fortnightly. Data on milk yield and lactation stage parameters were also available for each animal. We compared the performance of three prediction approaches: partial least-squares regression, support vector machine regression and random forest regression. The full milk MIRS alone gave low to moderate prediction accuracy (R2 = 0.07-0.40), regardless of prediction modelling approach. Adding more variables to the model improved R2 and decreased the prediction error. Overall, partial least-squares regression proved to be the best method for predicting DMI from milk MIRS data, while MIRS data together with milk yield and concentrate DMI at 3-30 d in milk provided good prediction accuracy (R2 = 0.52-0.65) regardless of the prediction tool used.

Phenotypic Analysis of Fourier-Transform Infrared Milk Spectra in Dairy Goats

The infrared spectrum of bovine milk is used to predict many interesting traits, whereas there have been few studies on goat milk in this regard. The objective of this study was to characterize the major sources of variation in the absorbance of the infrared spectrum in caprine milk samples. A total of 657 goats belonging to 6 breeds and reared on 20 farms under traditional and modern dairy systems were milk-sampled once. Fourier-transform infrared (FTIR) spectra were taken (2 replicates per sample, 1314 spectra), and each spectrum contained absorbance values at 1060 different wavenumbers (5000 to 930 × cm^-1), which were treated as a response variable and analyzed one at a time (i.e., 1060 runs). A mixed model, including the random effects of sample/goat, breed, flock, parity, stage of lactation, and the residual, was used. The pattern and variability of the FTIR spectrum of caprine milk was similar to those of bovine milk. The major sources of variation in the entire spectrum were as follows: sample/goat (33% of the total variance); flock (21%); breed (15%); lactation stage (11%); parity (9%); and the residual unexplained variation (10%). The entire spectrum was segmented into five relatively homogeneous regions. Two of them exhibited very large variations, especially the residual variation. These regions are known to be affected by the absorbance of water, although they also exhibited wide variations in the other sources of variation. The average repeatability of these two regions were 45% and 75%, whereas for the other three regions it was about 99%. The FTIR spectrum of caprine milk could probably be used to predict several traits and to authenticate the origin of goat milk.

Predicting nitrogen use efficiency, nitrogen loss and dry matter intake of individual dairy cows in late lactation by including mid-infrared spectra of milk samples

BACKGROUND

Nitrate leaching to groundwater and surface water and ammonia volatilization from dairy farms have negative impacts on the environment. Meanwhile, the increasing demand for dairy products will result in more pollution if N losses are not controlled. Therefore, a more efficient, and environmentally friendly production system is needed, in which nitrogen use efficiency (NUE) of dairy cows plays a key role. To genetically improve NUE, extensively recorded and cost-effective proxies are essential, which can be obtained by including mid-infrared (MIR) spectra of milk in prediction models for NUE. This study aimed to develop and validate the best prediction model of NUE, nitrogen loss (NL) and dry matter intake (DMI) for individual dairy cows in China.

RESULTS

A total of 86 lactating Chinese Holstein cows were used in this study. After data editing, 704 records were obtained for calibration and validation. Six prediction models with three different machine learning algorithms and three kinds of pre-processed MIR spectra were developed for each trait. Results showed that the coefficient of determination (R²) of the best model in within-herd validation was 0.66 for NUE, 0.58 for NL and 0.63 for DMI. For external validation, reasonable prediction results were only observed for NUE, with R² ranging from 0.58 to 0.63, while the R² of the other two traits was below 0.50. The infrared waves from 973.54 to 988.46 cm^-1 and daily milk yield were the most important variables for prediction.

CONCLUSION

The results showed that individual NUE can be predicted with a moderate accuracy in both within-herd and external validations. The model of NUE could be used for the datasets that are similar to the calibration dataset. The prediction models for NL and 3-day moving average of DMI (DMI_a) generated lower accuracies in within-herd validation. Results also indicated that information of MIR spectra variables increased the predictive ability of models. Additionally, pre-processed MIR spectra do not result in higher accuracy than original MIR spectra in the external validation. These models will be applied to large-scale data to further investigate the genetic architecture of N efficiency and further reduce the adverse impacts on the environment after more data is collected.

Fourier transform mid-infrared milk screening to improve milk production and processing

Milk mid-infrared spectrometry has been used for many years to quantify major milk compounds. Recently, much research has been conducted to extend the use of this technology to predict new, relevant phenotypes to assess the animals' welfare and the nutritional quality of milk, as well as its technological quality and environmental footprint. The transition from the research stage to field implementation is not easy, due to intrinsic and extrinsic constraints, but some developments can be considered to address these issues.

Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls

The purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.

Prediction of nitrogen excretion from data on dairy cows fed a wide range of diets compiled in an intercontinental database: A meta-analysis

Manure nitrogen (N) from cattle contributes to nitrous oxide and ammonia emissions and nitrate leaching. Measurement of manure N outputs on dairy farms is laborious, expensive, and impractical at large scales; therefore, models are needed to predict N excreted in urine and feces. Building robust prediction models requires extensive data from animals under different management systems worldwide. Thus, the study objectives were (1) to collate an international database of N excretion in feces and urine based on individual lactating dairy cow data from different continents; (2) to determine the suitability of key variables for predicting fecal, urinary, and total manure N excretion; and (3) to develop robust and reliable N excretion prediction models based on individual data from lactating dairy cows consuming various diets. A raw data set was created based on 5,483 individual cow observations, with 5,420 fecal N excretion and 3,621 urine N excretion measurements collected from 162 in vivo experiments conducted by 22 research institutes mostly located in Europe (n = 14) and North America (n = 5). A sequential approach was taken in developing models with increasing complexity by incrementally adding variables that had a significant individual effect on fecal, urinary, or total manure N excretion. Nitrogen excretion was predicted by fitting linear mixed models including experiment as a random effect. Simple models requiring dry matter intake (DMI) or N intake performed better for predicting fecal N excretion than simple models using diet nutrient composition or milk performance parameters. Simple models based on N intake performed better for urinary and total manure N excretion than those based on DMI, but simple models using milk urea N (MUN) and N intake performed even better for urinary N excretion. The full model predicting fecal N excretion had similar performance to simple models based on DMI but included several independent variables (DMI, diet crude protein content, diet neutral detergent fiber content, milk protein), depending on the location, and had root mean square prediction errors as a fraction of the observed mean values of 19.1% for intercontinental, 19.8% for European, and 17.7% for North American data sets. Complex total manure N excretion models based on N intake and MUN led to prediction errors of about 13.0% to 14.0%, which were comparable to models based on N intake alone. Intercepts and slopes of variables in optimal prediction equations developed on intercontinental, European, and North American bases differed from each other, and therefore region-specific models are preferred to predict N excretion. In conclusion, region-specific models that include information on DMI or N intake and MUN are required for good prediction of fecal, urinary, and total manure N excretion. In absence of intake data, region-specific complex equations using easily and routinely measured variables to predict fecal, urinary, or total manure N excretion may be used, but these equations have lower performance than equations based on intake.

Nitrogen isotopic discrimination as a biomarker of between-cow variation in the efficiency of nitrogen utilization for milk production: A meta-analysis

Estimating the efficiency of N utilization for milk production (MNE) of individual cows at a large scale is difficult, particularly because of the cost of measuring feed intake. Nitrogen isotopic discrimination (Δ¹⁵N) between the animal (milk, plasma, or tissues) and its diet has been proposed as a biomarker of the efficiency of N utilization in a range of production systems and ruminant species. The aim of this study was to assess the ability of Δ¹⁵N to predict the between-animal variability in MNE in dairy cows using an extensive database. For this, 20 independent experiments conducted as either changeover (n = 14) or continuous (n = 6) trials were available and comprised an initial data set of 1,300 observations. Between-animal variability was defined as the variation observed among cows sharing the same contemporary group (CG; individuals from the same experimental site, sampling period, and dietary treatment). Milk N efficiency was calculated as the ratio between mean milk N (grams of N in milk per day) and mean N intake (grams of N intake per day) obtained from each sampling period, which lasted 9.0 ± 9.9 d (mean ± SD). Samples of milk (n = 604) or plasma (n = 696) and feeds (74 dietary treatments) were analyzed for natural ¹⁵N abundance (δ¹⁵N), and then the N isotopic discrimination between the animal and the dietary treatment was calculated (Δ¹⁵n = δ¹⁵N_animal - δ¹⁵N_diet). Data were analyzed through mixed-effect regression models considering the experiment, sampling period, and dietary treatment as random effects. In addition, repeatability estimates were calculated for each experiment to test the hypothesis of improved predictions when MNE and Δ¹⁵N measurements errors were lower. The considerable protein mobilization in early lactation artificially increased both MNE and Δ¹⁵N, leading to a positive rather than negative relationship, and this limited the implementation of this biomarker in early lactating cows. When the experimental errors of Δ¹⁵N and MNE decreased in a particular experiment (i.e., higher repeatability values), we observed a greater ability of Δ¹⁵N to predict MNE at the individual level. The predominant negative and significant correlation between Δ¹⁵N and MNE in mid- and late lactation demonstrated that on average Δ¹⁵N reflects MNE variations both across dietary treatments and between animals. The root mean squared prediction error as a percentage of average observed value was 6.8%, indicating that the model only allowed differentiation between 2 cows in terms of MNE within a CG if they differed by at least 0.112 g/g of MNE (95% confidence level), and this could represent a limitation in predicting MNE at the individual level. However, the one-way ANOVA performed to test the ability of Δ¹⁵N to differentiate within-CG the top 25% from the lowest 25% individuals in terms of MNE was significant, indicating that it is possible to distinguish extreme animals in terms of MNE from their N isotopic signature, which could be useful to group animals for precision feeding.

Multiple Country Approach to Improve the Test-Day Prediction of Dairy Cows' Dry Matter Intake

Simple Summary

Dry matter intake, related to the number of nutrients available to an animal to meet its production and health needs, is crucial for the economic, environmental, and welfare management of dairy herds. Because the equipment required to weigh the ingested food at an individual level is not broadly available, we propose some new ways to approach the actual dry matter consumed by a dairy cow for a given day. To do so, we used regression models using parity (number of lactations), week of lactation, milk yield, milk mid-infrared spectrum, and prediction of bodyweight, fat, protein, lactose, and fatty acids content in milk. We chose these elements to predict individual dry matter intake because they are either easily accessible or routinely provided by regional dairy organizations (often called “dairy herd improvement” associations). We succeeded in producing a model whose dry matter intake predictions were moderately related to the actual values.

Abstract

We predicted dry matter intake of dairy cows using parity, week of lactation, milk yield, milk mid-infrared (MIR) spectrum, and MIR-based predictions of bodyweight, fat, protein, lactose, and fatty acids content in milk. The dataset comprised 10,711 samples of 534 dairy cows with a geographical diversity (Australia, Canada, Denmark, and Ireland). We set up partial least square (PLS) regressions with different constructs and a one-hidden-layer artificial neural network (ANN) using the highest contribution variables. In the ANN, we replaced the spectra with their projections to the 25 first PLS factors explaining 99% of the spectral variability to reduce the model complexity. Cow-independent 10 × 10-fold cross-validation (CV) achieved the best performance with root mean square errors (RMSE_CV) of 3.27 ± 0.08 kg for the PLS regression and 3.25 ± 0.13 kg for ANN. Although the available data were significantly different, we also performed a country-independent validation (CIV) to measure the models’ performance fairly. We found RMSE_CIV varying from 3.73 to 6.03 kg for PLS and 3.69 to 5.08 kg for ANN. Ultimately, based on the country-independent validation, we discussed the developed models’ performance with those achieved by the National Research Council’s equation.

Validation of Dairy Cow Bodyweight Prediction Using Traits Easily Recorded by Dairy Herd Improvement Organizations and Its Potential Improvement Using Feature Selection Algorithms

Knowing the body weight (BW) of a cow at a specific moment or measuring its changes through time is of interest for management purposes. The current work aimed to validate the feasibility of predicting BW using the day in milk, parity, milk yield, and milk mid-infrared (MIR) spectrum from a multiple-country dataset and reduce the number of predictors to limit the risk of over-fitting and potentially improve its accuracy. The BW modeling procedure involved feature selections and herd-independent validation in identifying the most interesting subsets of predictors and then external validation of the models. From 1849 records collected in 9 herds from 360 Holstein cows, the best performing models achieved a root mean square error (RMSE) for the herd-independent validation between 52 ± 2.34 kg to 56 ± 3.16 kg, including from 5 to 62 predictors. Among these models, three performed remarkably well in external validation using an independent dataset (N = 4067), resulting in RMSE ranging from 52 to 56 kg. The results suggest that multiple optimal BW predictive models coexist due to the high correlations between adjacent spectral points.

Appropriate Data Quality Checks Improve the Reliability of Values Predicted from Milk Mid-Infrared Spectra

Simple Summary

There is a growing interest in using milk mid-infrared (MIR) spectrometry to obtain new phenotypes to assist in the complex management of dairy farms. These predictive values can be erroneous for many reasons, even if the prediction equations used are accurate. Unfortunately, there is no quality protocol routinely implemented to detect those abnormal predictive values in the database recorded by dairy herd improvement (DHI) organizations, except for fat and protein contents. However, for financial and practical reasons, it is unfeasible to adapt the quality protocol commonly used in milk laboratories to improve the accuracy of those traits. So, this study proposes three different statistical methods that would be easy to implement by DHI organizations to detect abnormal values and limit the spectral extrapolation in order to improve the accuracy of MIR-based predictive values.

Abstract

The use of abnormal milk mid-infrared (MIR) spectrum strongly affects prediction quality, even if the prediction equations used are accurate. So, this record must be detected after or before the prediction process to avoid erroneous spectral extrapolation or the use of poor-quality spectral data by dairy herd improvement (DHI) organizations. For financial or practical reasons, adapting the quality protocol currently used to improve the accuracy of fat and protein contents is unfeasible. This study proposed three different statistical methods that would be easy to implement by DHI organizations to solve this issue: the deletion of 1% of the extreme high and low predictive values (M1), the deletion of records based on the Global-H (GH) distance (M2), and the deletion of records based on the absolute fat residual value (M3). Additionally, the combinations of these three methods were investigated. A total of 346,818 milk samples were analyzed by MIR spectrometry to predict the contents of fat, protein, and fatty acids. Then, the same traits were also predicted externally using their corresponded standardized MIR spectra. The interest in cleaning procedures was assessed by estimating the root mean square differences (RMSDs) between those internal and external predicted phenotypes. All methods allowed for a decrease in the RMSD, with a gain ranging from 0.32% to 41.39%. Based on the obtained results, the “M1 and M2” combination should be preferred to be more parsimonious in the data loss, as it had the higher ratio of RMSD gain to data loss. This method deleted the records based on the 2% extreme predictions and a GH threshold set at 5. However, to ensure the lowest RMSD, the “M2 or M3” combination, considering a GH threshold of 5 and an absolute fat residual difference set at 0.30 g/dL of milk, was the most relevant. Both combinations involved M2 confirming the high interest of calculating the GH distance for all samples to predict. However, if it is impossible to estimate the GH distance due to a lack of relevant information to compute this statistical parameter, the obtained results recommended the use of M1 combined with M3. The limitation used in M3 must be adapted by the DHI, as this will depend on the spectral data and the equation used. The methodology proposed in this study can be generalized for other MIR-based phenotypes.

Estimation of genetic parameters for predicted nitrogen use efficiency and losses in early lactation of Holstein cows

The objective of this study was to estimate genetic parameters of predicted N use efficiency (PNUE) and N losses (PNL) as proxies of N use and loss for Holstein cows. Furthermore, we have assessed approximate genetic correlations between PNUE, PNL, and dairy production, health, longevity, and conformation traits. These traits are considered important in many countries and are currently evaluated by the International Bull Evaluation Service (Interbull). The values of PNUE and PNL were obtained by using the combined milk mid-infrared (MIR) spectrum, parity, and milk yield-based prediction equations on test-day MIR records with days in milk (DIM) between 5 and 50 d. After editing, the final data set comprised 46,163 records of 21,462 cows from 154 farms in 5 countries. Each trait was divided into primiparous and multiparous (including second to fifth parity) groups. Genetic parameters and breeding values were estimated by using a multitrait (2-trait, 2-parity classes) repeatability model. Herd-year-season of calving, DIM, age of calving, and parity were used as fixed effects. Random effects were defined as parity (within-parity permanent environment), nongenetic cow (across-parity permanent environment), additive genetic animal, and residual effects. The estimated heritability of PNUE and PNL in the first and later parity were 0.13, 0.12, 0.14, and 0.13, and the repeatability values were 0.49, 0.40, 0.55, and 0.43, respectively. The estimated approximate genetic correlations between PNUE and PNL were negative and high (from -0.89 to -0.53), whereas the phenotypic correlations were also negative but relatively low (from -0.45 to -0.11). At a level of reliability of more than 0.30 for all novel traits, a total of 504 bulls born after 1995 had also publishable Interbull multiple-trait across-country estimated breeding values (EBV). The approximate genetic correlations between PNUE and the other 30 traits of interest, estimated as corrected correlations between EBV of bulls, ranged from -0.46 (udder depth) to 0.47 (milk yield). Obtained results showed the complex genetic relationship between efficiency, production, and other traits: for instance, more efficient cows seem to give more milk, which is linked to deeper udders, but seem to have lower health, fertility, and longevity. Additionally, the approximate genetic correlations between PNL, lower values representing less loss of N, and the 30 other traits, were from -0.32 (angularity) to 0.57 (direct calving ease). Even if further research is needed, our results provided preliminary evidence that the PNUE and PNL traits used as proxies could be included in genetic improvement programs in Holstein cows and could help their management.

Proxy Measures and Novel Strategies for Estimating Nitrogen Utilisation Efficiency in Dairy Cattle

Simple Summary

Dairy cow diets contain nitrogen, mostly in the form of protein. However, dietary nitrogen is used with a low efficiency for milk production, and much of the unused nitrogen is converted to urea and excreted in urine and faeces (manure). Nitrogen within manure can then be lost to the environment, and this is a particular issue when dairy cows are offered diets containing excess dietary protein. As a result, there is increasing pressure on the dairy sector to improve the efficiency with which dairy cows utilise dietary nitrogen. While nitrogen utilisation efficiency can be measured accurately on research farms, this is more difficult on commercial farms. For that reason, there is much interest in developing low-cost and easy-to-use proximate measures that can provide accurate estimates of nitrogen utilisation. This review examines a number of proximate analyses that are already used as indicators of nitrogen use efficiency in dairy cows (e.g., blood urea and milk urea), and a number of more novel measures that may have potential for use in the future (including analysis of milk, blood, urine, breath, and predictions of intake). These ‘proxy’ measurements can be used to improve feeding management and might be used to monitor adherence to legislation.

Abstract

The efficiency with which dairy cows convert dietary nitrogen (N) to milk N is generally low (typically 25%). As a result, much of the N consumed is excreted in manure, from which N can be lost to the environment. Therefore there is increasing pressure to reduce N excretion and improve N use efficiency (NUE) on dairy farms. However, assessing N excretion and NUE on farms is difficult, thus the need to develop proximate measures that can provide accurate estimates of nitrogen utilisation. This review examines a number of these proximate measures. While a strong relationship exists between blood urea N and urinary N excretion, blood sampling is an invasive technique unsuitable for regular herd monitoring. Milk urea N (MUN) can be measured non-invasively, and while strong relationships exist between dietary crude protein and MUN, and MUN and urinary N excretion, the technique has limitations. Direct prediction of NUE using mid-infrared analysis of milk has real potential, while techniques such as near-infrared spectroscopy analysis of faeces and manure have received little attention. Similarly, techniques such as nitrogen isotope analysis, nuclear magnetic resonance spectroscopy of urine, and breath ammonia analysis may all offer potential in the future, but much research is still required.

Infrared Spectrometry as a High-Throughput Phenotyping Technology to Predict Complex Traits in Livestock Systems

High-throughput phenotyping technologies are growing in importance in livestock systems due to their ability to generate real-time, non-invasive, and accurate animal-level information. Collecting such individual-level information can generate novel traits and potentially improve animal selection and management decisions in livestock operations. One of the most relevant tools used in the dairy and beef industry to predict complex traits is infrared spectrometry, which is based on the analysis of the interaction between electromagnetic radiation and matter. The infrared electromagnetic radiation spans an enormous range of wavelengths and frequencies known as the electromagnetic spectrum. The spectrum is divided into different regions, with near- and mid-infrared regions being the main spectral regions used in livestock applications. The advantage of using infrared spectrometry includes speed, non-destructive measurement, and great potential for on-line analysis. This paper aims to review the use of mid- and near-infrared spectrometry techniques as tools to predict complex dairy and beef phenotypes, such as milk composition, feed efficiency, methane emission, fertility, energy balance, health status, and meat quality traits. Although several research studies have used these technologies to predict a wide range of phenotypes, most of them are based on Partial Least Squares (PLS) and did not considered other machine learning (ML) techniques to improve prediction quality. Therefore, we will discuss the role of analytical methods employed on spectral data to improve the predictive ability for complex traits in livestock operations. Furthermore, we will discuss different approaches to reduce data dimensionality and the impact of validation strategies on predictive quality.

Large-scale phenotyping in dairy sector using milk MIR spectra: Key factors affecting the quality of predictions

Methods and technologies enabling the estimation at large scale of important traits for the dairy sector are of great interest. Those phenotypes are necessary to improve herd management, animal genetic evaluation, and milk quality control. In the recent years, the research was very active to predict new phenotypes from the mid-infrared (MIR) analysis of milk. Models were developed to predict phenotypes such as fine milk composition, milk technological properties or traits related to cow health, fertility and environmental impact. Most of models were developed within research contexts and often not designed for routine use. The implementation of models at a large scale to predict new traits of interest brings new challenges as the factors influencing the robustness of models are poorly documented. The first objective of this work is to highlight the impact on prediction accuracy of factors such as the variability of the spectral and reference data, the spectral regions used and the complexity of models. The second objective is to emphasize methods and indicators to evaluate the quality of models and the quality of predictions generated under routine conditions. The last objective is to outline the issues and the solutions linked with the use and transfer of models on large number of instruments. Based on partial least square regression and 10 datasets including milk MIR spectra and reference quantitative values for 57 traits of interest, the impact of the different factors is illustrated by evaluating the influence on the validation root mean square error of prediction (RMSEP). In the displayed examples, all factors, when well set up, increase the quality of predictions, with an improvement of the RMSEP ranging from 12% to 43%. This work also aims to underline the need for and the complementarity between different validation procedures, statistical parameters and quality assurance methods. Finally, when using and transferring models, the impact of the spectral standardization on the prediction reproducibility is highlighted with an improvement up to 86% with the tested models, and the monitoring of individual spectrometer stability over time appears essential. This list inspired from our experience is of course not exhaustive. The displayed results are only examples and not general rules and other aspects play a role in the quality of final predictions. However, this work highlights good practices, methods and indicators to increase and evaluate quality of phenotypes predicted at a large scale. The results obtained argue for the development of guidelines at international levels, as well as international collaborations in order to constitute large and robust datasets and enable the use of models in routine conditions.