Modeling genetic and nongenetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors

Impact of parity differences on residual feed intake estimation in Holstein cows

Residual feed intake (RFI) has been used as a measure of feed efficiency in farm animals. In lactating dairy cattle, RFI is typically obtained as the difference between dry matter intake observations and predictions from regression on known energy sinks, and effects of parity, days in milk, and cohort. The impact of parity (lactation number) on the estimation of RFI is not well understood, so the objectives of this study were to (1) evaluate alternative RFI models in which the energy sinks (metabolic body weight, body weight change, and secreted milk energy) were nested or not nested within parity, and (2) estimate variance components and genetic correlations for RFI across parities. Data consisted of 72,474 weekly RFI records of 5,813 lactating Holstein cows collected from 2007 to 2022 in 5 research stations across the United States. Estimates of heritability, repeatability, and genetic correlations between weekly RFI for parities 1, 2, and 3 were obtained using bivariate repeatability animal models. The nested RFI model showed better goodness of fit than the nonnested model, and some partial regression coefficients of dry matter intake on energy sinks were heterogeneous between parities. However, the Spearman's rank correlation between RFI values calculated from nested and nonnested models was equal to 0.99. Similarly, Spearman's rank correlation between the RFI breeding values from these 2 models was equal to 0.98. Heritability estimates for RFI were equal to 0.16 for parity 1, 0.19 for parity 2, and 0.22 for parity 3. Repeatability estimates for RFI across weeks within parities were high, ranging from 0.51 to 0.57. Spearman's rank correlations of sires' breeding values were 0.99 between parities 1 and 2, 0.91 between parities 1 and 3, and 0.92 between parities 2 and 3. We conclude that nesting energy sinks within parity when computing RFI improves model goodness of fit, but the impact on the estimated breading values appears to be minimal.

The Effect of Short-Wavelength White LED Illumination throughout the Night on the Milk Fatty Acid Profile of High-Yielding Dairy Cows

Fatty acid levels in milk vary between day and night milking. Many dairy cows are still kept under white light-emitting diode (W-LED) illumination throughout the night, although it is known to disrupt endogenous circadian rhythms. We investigated the effects of whole-night W-LED illumination (125 lux) on milk yield and circadian composition, compared to a natural light−dark (LD) cycle of 10 h light. Mid−late lactation cows (n = 34) that were exposed to natural LD cycle showed circadian variation in milk fat composition, characterized by higher health-promoting monounsaturated fatty acid (MUFA; 24.2 ± 0.4 vs. 23.2 ± 0.4 g/100 g fat, p < 0.001) and lower saturated fatty acid levels (71.2 ± 0.4 vs. 72.5 ± 0.4, p < 0.001) at 13:30 h (day milk) than at 03:30 h (night milk). Compared to natural LD (n = 16), W-LED (n = 18) did not affect milk production or milk fat yields, yet abolished the milking time variation in milk fat composition towards a less healthy fatty acid profile. This lowered MUFA levels of day milk (23.8 ± 0.4 vs. 26.7 ± 0.4, p < 0.01). Therefore, W-LED has no commercial advantage over the tested natural LD cycle, and conversely, even shows circadian disruption. Accordingly, a natural LD cycle of 10 h light is preferable over W-LED from the perspective of cost savings, the cows’ well-being, and preserving the natural milk fat profile, as the nutritional value of the day milk is slightly higher.

Combining datasets in a dynamic residual feed intake model and comparison with linear model results in lactating Holstein cattle

A new method to estimate residual feed intake (RFI) was recently developed based on a multi-trait random regression model. This approach deals with the dynamic nature of the lactation, which is in contrast with classical linear approaches. However, an issue remains: pooling data across sites and years, which implies dealing with different (and sometimes unknown) diet energy contents. This will be needed for genomic evaluation. In this study, we tested whether merging two individual datasets into a larger one can lead to valuable results in comparison to analysing them on their own with the multi-trait random regression model. Three datasets were defined: the first one with 1 063 lactations, the second one with 205 lactations from a second farm and the third one combining the data of the two first datasets (1 268 lactations). The model was applied to the three datasets to estimate individual RFI as well as variance components and correlations between the four traits included in the model (fat and protein corrected milk production, BW, feed intake and body condition score), and a fixed month-year-farm effect was used to define the contemporary group. The variance components and correlations between animal effects of the four traits were very similar irrespective of the dataset used with correlations higher than 0.94 between the different datasets. The RFI estimates for animals from their single farm only were also very similar (r > 0.95) to the ones computed from the merged dataset (Dataset 3). This highlights that the contemporary group correction in the model adequately accounts for differences between the two feeding environments. The dynamic model can thus be used to produce RFI estimates from merged datasets, at least when animals are raised in similar systems. In addition, the 205 lactations from the second farm were also used to estimate the RFI with a linear approach. The RFI estimated by the two approaches were similar when the considered period was rather short (r = 0.85 for RFI for the first 84 days of lactation) but this correlation weakened as the period length grew (r = 0.77 for RFI for the first 168 days of lactation). This weakening in correlations between the two approaches when increasing the used time-period reflects that only the dynamic model permits the regression coefficients to evolve in line with the physiological changes through the lactation. The results of this study enlarge the possibilities of use for the dynamic RFI model.

Amino Acid Metabolomic Profiles in Bovine Mammary Epithelial Cells under Essential Amino Acid Restriction

Simple Summary

Cells of the mammary gland obtain their necessary nutrients from the blood to produce milk components, such as casein. To achieve higher productivity, cows are excessively supplemented, thus generating a higher cost of production and affecting the environment. Therefore, this triggers the need for a reduction in the supplementation of essential amino acids without affecting the milk composition. The present in vitro study shows that, through homeostatic and homeorhetic processes, cells have the ability to maintain stable casein levels despite decreasing the percentage of essential amino acids (EAAs) supplied. These findings could contribute to the proposal of more efficient nutritional strategies at lower environmental and economic costs.

Abstract

Mammary epithelial cells (MECs) in culture are a useful model for elucidating mammary gland metabolism and changes that occur under different nutrient disponibility. MECs were exposed to different treatments: 100% EAA for 8 h and 24 h restriction (R); 2% EAA for 8 h and 24 h R; 2% EAA for 8 h and 24 h + 100% EAA for 8 h and 24 h restriction + re-feeding (R + RF). Western blotting and protein quantification was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) software identified the amino acids (AAs) and signaling pathways. The chi-squared test, multiple classification analysis, and analysis of variance were used for the purification and identification of data. Intracellular casein levels were not affected. The KEGG analysis revealed that the important pathways of metabolism of AAs, which were involved in processes related to metabolism and biosynthesis of phenylalanine, tyrosine, and tryptophan (fumarate, acetyl-CoA, and tricarboxylic acid (TCA) cycle), were affected by both R and R + RF treatments, mainly through the glutamic-oxaloacetic transaminase-2 enzyme. Additionally, metabolic processes mediated by the mitochondrial malate dehydrogenase, S-adenosylmethionine synthetase, and asparagine synthase proteins positively regulated the carbohydrate pathway, pyruvate, and TCA cycles, as well as the metabolism of alanine, aspartate, and glutamate metabolism (carbohydrate and TCA cycle). We hypothesized that MECs have the capacity to utilize alternative pathways that ensure the availability of substrates for composing milk proteins.

Invited review: Disentangling residual feed intake-Insights and approaches to make it more fit for purpose in the modern context

Residual feed intake (RFI) is an increasingly used trait to analyze feed efficiency in livestock, and in some sectors such as dairy cattle, it is one of the most frequently used traits. Although the principle for calculating RFI is always the same (i.e., using the residual of a regression of intake on performance predictors), a wide range of models are found in the literature, with different predictors, different ways of considering intake, and more recently, different statistical approaches. Consequently, the results are not easily comparable from one study to another as they reflect different biological variabilities, and the relationship between the residual (i.e., RFI) and the underlying true efficiency also differs. In this review, the components of the RFI equation are explored with respect to the underlying biological processes. The aim of this decomposition is to provide a better understanding of which of the processes in this complex trait contribute significantly to the individual variability in efficiency. The intricacies associated with the residual term, as well as the energy sinks and the intake term, are broken down and discussed. Based on this exploration as well as on some recent literature, new forms of the RFI equation are proposed to better separate the efficiency terms from errors and inaccuracies. The review also considers the time period of measurement of RFI. This is a key consideration for the accuracy of the RFI estimation itself, and also for understanding the relationships between short-term efficiency, animal resilience, and long-term efficiency. As livestock production moves toward sustainable efficiency, these considerations are increasingly important to bring to bear in RFI estimations.

A new method to estimate residual feed intake in dairy cattle using time series data

In dairy, the usual way to measure feed efficiency is through the residual feed intake (RFI) method. However, this method is, in its classical form, a linear regression, which, by construction, does not take into account the evolution of the RFI components across time, inducing approximations in the results. We present here a new approach that incorporates the dynamic dimension of the data. Using a multitrait random regression model, the correlations between milk, live weight, DM intake (DMI) and body condition score (BCS) were investigated across the lactation. In addition, at each time point, by a matrix regression on the variance-covariance matrix and on the animal effects from the three predictor traits, a predicted animal effect for intake was estimated, which, by difference with the actual animal effect for intake, gave a RFI estimation. This model was tested on historical data from the Aarhus University experimental farm (1 469 lactations out of 740 cows). Correlations between animal effects were positive and high for milk and DMI and for weight and DMI, with a maximum mid-lactation, stable across time at around 0.4 for weight and BCS, and slowly decreasing along the lactation for milk and weight, DMI and BCS, and milk and BCS. At the Legendre polynomial coefficient scale, the correlations were estimated with a high accuracy (averaged SE of 0.04, min = 0.02, max = 0.05). The predicted animal effect for intake was always extremely highly correlated with the milk production and highly correlated with BW for the most part of the lactation, but only slightly correlated with BCS, with the correlation becoming negative in the second half of the lactation. The estimated RFI possessed all the characteristics of a classical RFI, with a mean at zero at each time point and a phenotypic independence from its predictors. The correlation between the averaged RFI over the lactation and RFI at each time point was always positive and above 0.5, and maximum mid-lactation (>0.9). The model performed reasonably well in the presence of missing data. This approach allows a dynamic estimation of the traits, free from all time-related issues inherent to the traditional RFI methodology, and can easily be adapted and used in a genetic or genomic selection context.

Updating predictions of dry matter intake of lactating dairy cows

Our objective was to model dry matter intake (DMI) by Holstein dairy cows based on milk energy (MilkE), body weight (BW), change in BW (ΔBW), body condition score (BCS), height, days in milk (DIM), and parity (primiparous and multiparous). Our database included 31,631 weekly observations on 2,791 cows enrolled in 52 studies from 8 states of the United States, mostly in the Upper Midwest. The means ± standard deviations of these variables were 24 ± 5 kg of DMI, 30 ± 6 Mcal of MilkE/d, 624 ± 83 kg of BW, 0.24 ± 1.50 kg of ΔBW/d, 3.0 ± 0.5 BCS, 149 ± 6 cm height, and 102 ± 45 DIM. Data analysis was performed using a mixed-effects model containing location, study within location, diet within study, and location and cow within study as random effects, whereas the fixed effects included the linear effects of the covariates described previously and all possible 2-way interactions between parity and the other covariates. A nonlinear (NLIN) mixed model analysis was developed using a 2-step approach for computational tractability. In the first step, we used a linear (LIN) model component of the NLIN model to predict DMI using only data from mid-lactation dairy cows (76-175 DIM) without including information on DIM. In the second step, a nonlinear adjustment for DIM using all data from 0 to 368 DIM was estimated. Additionally, this NLIN model was compared with an LIN model containing a fourth-order polynomial for DIM using data throughout the entire lactation (0-368 DIM) to assess the utility of an NLIN model for the prediction of DMI. In summary, a total of 8 candidate models were evaluated as follows: 4 ways to express energy required for maintenance (BW, BW^0.75, BW adjusted for a BCS of 3, and BW^0.75 adjusted for a BCS of 3) × 2 modeling strategies (LIN vs. NLIN). The candidate models were compared using a 5-fold across-studies cross-validation approach repeated 20 times with the best-fitting model chosen as the proposed model. The metrics used for evaluation were the mean bias, slope bias, concordance correlation coefficient (CCC), and root mean squared error of prediction (RMSEP). The proposed prediction equation was DMI (kg/d) = [(3.7 + parity × 5.7) + 0.305 × MilkE (Mcal/d) + 0.022 × BW (kg) + (-0.689 + parity × -1.87) × BCS] × [1 - (0.212 + parity × 0.136) × exp^{(-0.053 × DIM)}] (mean bias = 0.021 kg, slope bias = 0.059, CCC = 0.72, and RMSEP = 2.89 kg), where parity is equal to 1 if the animal is multiparous and 0 otherwise. Finally, the proposed model was compared against the Nutrient Requirements of Dairy Cattle (2001) prediction equation for DMI using an independent data set of 9,050 weekly observations on 1,804 Holstein cows. The proposed model had smaller mean bias and RMSEP and higher CCC than the Nutrient Requirements of Dairy Cattle equation to predict DMI and has potential to improve diet formulation for lactating dairy cows.

Genome-wide association analyses based on a multiple-trait approach for modeling feed efficiency

Genome-wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 cows from 16 stations in 4 counties. Of these cows, 4,916 had genotypes on 57,347 single nucleotide polymorphism (SNP) markers. We compared a GWA analysis based on the more classical residual feed intake (RFI) model with one based on a previously proposed multiple trait (MT) approach for modeling FE using an alternative measure (DMI|MILKE,MBW). Both models were based on a single-step genomic BLUP procedure that allowed the use of phenotypes from both genotyped and nongenotyped cows. Estimated effects for single SNP markers were small and not statistically important but virtually identical for either FE measure (RFI vs. DMI|MILKE,MBW). However, upon further refining this analysis to develop joint tests within nonoverlapping 1-Mb windows, significant associations were detected between either measure of FE with a window on each of Bos taurus autosomes BTA12 and BTA26. There was, as expected, no overlap between detected genomic regions for DMI|MILKE,MBW and genomic regions influencing the energy sink traits (i.e., MILKE and MBW) because of orthogonal relationships clearly defined between the various traits. Conversely, GWA inferences on DMI can be demonstrated to be partly driven by genetic associations between DMI with these same energy sink traits, thereby having clear implications when comparing GWA studies on DMI to GWA studies on FE-like measures such as RFI.

Variation in residual feed intake depends on feed on offer

Two small pen trials with cattle and sheep both clearly demonstrated that while there is significant variation in residual feed intake when on high energy supply, there is negligible variation when energy supply is limited. A review of literature demonstrated that this is also the case when energy supply is limited by heat or physiological state, such as peak lactation, and in multiple species. There is little evidence of variation in efficiency of maintenance requirements, growth or lactation. Nor is there strong evidence for large variation in digestibility within breeds, despite some differences between divergent breeds. Thus, the primary source of variation in residual feed intake must be in appetite and, in variable environments, it is possible that those with greater appetite are more resilient during times of feed shortage.